DC-Build-Header: hhsuite 2.0.16-1 / 2014-06-17 13:15:48 +0000 DC-Task: source:hhsuite version:2.0.16-1 architecture:any chroot:unstable esttime:597 logfile:/tmp/hhsuite_2.0.16-1_unstable_clang.log modes:binary-only:parallel:clang DC-Sbuild-call: su user -c 'sbuild -n --apt-update -d unstable -v --chroot-setup-commands=/tmp/switch-to-clang --append-to-version "clang1" --maintainer "Lucas Nussbaum " --uploader "Lucas Nussbaum " hhsuite_2.0.16-1' sbuild (Debian sbuild) 0.63.2 (18 Aug 2012) on ip-172-31-4-82.us-west-2.compute.internal ╔══════════════════════════════════════════════════════════════════════════════╗ ║ hhsuite 2.0.16-1clang1 (amd64) 17 Jun 2014 13:15 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: hhsuite Version: 2.0.16-1clang1 Source Version: 2.0.16-1 Distribution: unstable Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 I: NOTICE: Log filtering will replace 'build/hhsuite-oE8KkS/hhsuite-2.0.16' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/hhsuite-oE8KkS' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/unstable-amd64-sbuild-296c1dd7-b3a3-419b-97de-8888214a3548' with '«CHROOT»' ┌──────────────────────────────────────────────────────────────────────────────┐ │ Update chroot │ └──────────────────────────────────────────────────────────────────────────────┘ Get:1 http://localhost:9999 unstable InRelease [206 kB] Get:2 http://localhost:9999 unstable/main Sources/DiffIndex [7876 B] Get:3 http://localhost:9999 unstable/main amd64 Packages/DiffIndex [7876 B] Get:4 http://localhost:9999 unstable/main Translation-en/DiffIndex [7876 B] Get:5 http://localhost:9999 unstable/main 2014-06-16-2054.31.pdiff [15.4 kB] Get:6 http://localhost:9999 unstable/main 2014-06-17-0253.05.pdiff [7983 B] Get:7 http://localhost:9999 unstable/main 2014-06-17-0856.27.pdiff [7757 B] Get:8 http://localhost:9999 unstable/main 2014-06-17-0856.27.pdiff [7757 B] Get:9 http://localhost:9999 unstable/main amd64 2014-06-16-2054.31.pdiff [20.7 kB] Get:10 http://localhost:9999 unstable/main amd64 2014-06-17-0253.05.pdiff [38.6 kB] Get:11 http://localhost:9999 unstable/main amd64 2014-06-17-0856.27.pdiff [9018 B] Get:12 http://localhost:9999 unstable/main 2014-06-16-2054.31.pdiff [699 B] Get:13 http://localhost:9999 unstable/main 2014-06-17-0856.27.pdiff [442 B] Get:14 http://localhost:9999 unstable/main amd64 2014-06-17-0856.27.pdiff [9018 B] Get:15 http://localhost:9999 unstable/main 2014-06-17-0856.27.pdiff [442 B] Fetched 330 kB in 5s (61.7 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following packages will be upgraded: libc-bin libc-dev-bin libc6 libc6-dev linux-libc-dev multiarch-support 6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 9447 kB of archives. After this operation, 10.2 kB of additional disk space will be used. Get:1 http://localhost:9999/debian/ unstable/main libc6-dev amd64 2.19-2 [2000 kB] Get:2 http://localhost:9999/debian/ unstable/main libc-dev-bin amd64 2.19-2 [235 kB] Get:3 http://localhost:9999/debian/ unstable/main linux-libc-dev amd64 3.14.7-1 [937 kB] Get:4 http://localhost:9999/debian/ unstable/main libc-bin amd64 2.19-2 [1288 kB] Get:5 http://localhost:9999/debian/ unstable/main libc6 amd64 2.19-2 [4816 kB] Get:6 http://localhost:9999/debian/ unstable/main multiarch-support amd64 2.19-2 [171 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 9447 kB in 0s (32.7 MB/s) (Reading database ... 14215 files and directories currently installed.) Preparing to unpack .../libc6-dev_2.19-2_amd64.deb ... Unpacking libc6-dev:amd64 (2.19-2) over (2.19-1) ... Preparing to unpack .../libc-dev-bin_2.19-2_amd64.deb ... Unpacking libc-dev-bin (2.19-2) over (2.19-1) ... Preparing to unpack .../linux-libc-dev_3.14.7-1_amd64.deb ... Unpacking linux-libc-dev:amd64 (3.14.7-1) over (3.14.5-1) ... Preparing to unpack .../libc-bin_2.19-2_amd64.deb ... Unpacking libc-bin (2.19-2) over (2.19-1) ... Preparing to unpack .../libc6_2.19-2_amd64.deb ... Unpacking libc6:amd64 (2.19-2) over (2.19-1) ... Setting up libc6:amd64 (2.19-2) ... Setting up libc-bin (2.19-2) ... (Reading database ... 14216 files and directories currently installed.) Preparing to unpack .../multiarch-support_2.19-2_amd64.deb ... Unpacking multiarch-support (2.19-2) over (2.19-1) ... Setting up multiarch-support (2.19-2) ... Setting up libc-dev-bin (2.19-2) ... Setting up linux-libc-dev:amd64 (3.14.7-1) ... Setting up libc6-dev:amd64 (2.19-2) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Fetch source files │ └──────────────────────────────────────────────────────────────────────────────┘ Check APT ───────── Checking available source versions... Download source files with APT ────────────────────────────── Reading package lists... Building dependency tree... Reading state information... NOTICE: 'hhsuite' packaging is maintained in the 'Svn' version control system at: svn://svn.debian.org/debian-med/trunk/packages/hhsuite/trunk/ Need to get 4350 kB of source archives. Get:1 http://localhost:9999/debian/ unstable/main hhsuite 2.0.16-1 (dsc) [2131 B] Get:2 http://localhost:9999/debian/ unstable/main hhsuite 2.0.16-1 (tar) [4338 kB] Get:3 http://localhost:9999/debian/ unstable/main hhsuite 2.0.16-1 (diff) [10.4 kB] Fetched 4350 kB in 2s (2065 kB/s) Download complete and in download only mode Check arch ────────── ┌──────────────────────────────────────────────────────────────────────────────┐ │ Chroot Setup Commands │ └──────────────────────────────────────────────────────────────────────────────┘ /tmp/switch-to-clang ──────────────────── + echo 'Entering customization script...' Entering customization script... + echo 'Install of clang-3.4' Install of clang-3.4 + apt-get update Hit http://localhost:9999 unstable InRelease Hit http://localhost:9999 unstable/main Sources/DiffIndex Hit http://localhost:9999 unstable/main amd64 Packages/DiffIndex Hit http://localhost:9999 unstable/main Translation-en/DiffIndex Reading package lists... + apt-get install --yes --no-install-recommends --force-yes clang-3.4 Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: libclang-common-3.4-dev libclang1-3.4 libffi6 libllvm3.4 libobjc-4.9-dev libobjc4 Suggested packages: gnustep gnustep-devel Recommended packages: llvm-3.4-dev python The following NEW packages will be installed: clang-3.4 libclang-common-3.4-dev libclang1-3.4 libffi6 libllvm3.4 libobjc-4.9-dev libobjc4 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. Need to get 30.6 MB of archives. After this operation, 118 MB of additional disk space will be used. Get:1 http://localhost:9999/debian/ unstable/main libffi6 amd64 3.1-2 [19.8 kB] Get:2 http://localhost:9999/debian/ unstable/main libllvm3.4 amd64 1:3.4.2-2 [6721 kB] Get:3 http://localhost:9999/debian/ unstable/main libobjc4 amd64 4.9.0-6 [112 kB] Get:4 http://localhost:9999/debian/ unstable/main libobjc-4.9-dev amd64 4.9.0-6 [372 kB] Get:5 http://localhost:9999/debian/ unstable/main libclang1-3.4 amd64 1:3.4.2-2 [3619 kB] Get:6 http://localhost:9999/debian/ unstable/main libclang-common-3.4-dev amd64 1:3.4.2-2 [543 kB] Get:7 http://localhost:9999/debian/ unstable/main clang-3.4 amd64 1:3.4.2-2 [19.2 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 30.6 MB in 0s (30.6 MB/s) Selecting previously unselected package libffi6:amd64. (Reading database ... 14216 files and directories currently installed.) Preparing to unpack .../libffi6_3.1-2_amd64.deb ... Unpacking libffi6:amd64 (3.1-2) ... Selecting previously unselected package libllvm3.4:amd64. Preparing to unpack .../libllvm3.4_1%3a3.4.2-2_amd64.deb ... Unpacking libllvm3.4:amd64 (1:3.4.2-2) ... Selecting previously unselected package libobjc4:amd64. Preparing to unpack .../libobjc4_4.9.0-6_amd64.deb ... Unpacking libobjc4:amd64 (4.9.0-6) ... Selecting previously unselected package libobjc-4.9-dev:amd64. Preparing to unpack .../libobjc-4.9-dev_4.9.0-6_amd64.deb ... Unpacking libobjc-4.9-dev:amd64 (4.9.0-6) ... Selecting previously unselected package libclang1-3.4:amd64. Preparing to unpack .../libclang1-3.4_1%3a3.4.2-2_amd64.deb ... Unpacking libclang1-3.4:amd64 (1:3.4.2-2) ... Selecting previously unselected package libclang-common-3.4-dev. Preparing to unpack .../libclang-common-3.4-dev_1%3a3.4.2-2_amd64.deb ... Unpacking libclang-common-3.4-dev (1:3.4.2-2) ... Selecting previously unselected package clang-3.4. Preparing to unpack .../clang-3.4_1%3a3.4.2-2_amd64.deb ... Unpacking clang-3.4 (1:3.4.2-2) ... Setting up libffi6:amd64 (3.1-2) ... Setting up libllvm3.4:amd64 (1:3.4.2-2) ... Setting up libobjc4:amd64 (4.9.0-6) ... Setting up libobjc-4.9-dev:amd64 (4.9.0-6) ... Setting up libclang1-3.4:amd64 (1:3.4.2-2) ... Setting up libclang-common-3.4-dev (1:3.4.2-2) ... Setting up clang-3.4 (1:3.4.2-2) ... Processing triggers for libc-bin (2.19-2) ... + echo 'Replace gcc, g++ & cpp by clang' Replace gcc, g++ & cpp by clang + VERSIONS='4.6 4.7 4.8 4.9' + cd /usr/bin + for VERSION in '$VERSIONS' + rm -f g++-4.6 gcc-4.6 cpp-4.6 + ln -s clang++ g++-4.6 + ln -s clang gcc-4.6 + ln -s clang cpp-4.6 + echo 'gcc-4.6 hold' + dpkg --set-selections + echo 'g++-4.6 hold' + dpkg --set-selections + for VERSION in '$VERSIONS' + rm -f g++-4.7 gcc-4.7 cpp-4.7 + ln -s clang++ g++-4.7 + ln -s clang gcc-4.7 + ln -s clang cpp-4.7 + echo 'gcc-4.7 hold' + dpkg --set-selections + echo 'g++-4.7 hold' + dpkg --set-selections + for VERSION in '$VERSIONS' + rm -f g++-4.8 gcc-4.8 cpp-4.8 + ln -s clang++ g++-4.8 + ln -s clang gcc-4.8 + ln -s clang cpp-4.8 + echo 'gcc-4.8 hold' + dpkg --set-selections dpkg: warning: package not in database at line 1: gcc-4.8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method + echo 'g++-4.8 hold' + dpkg --set-selections dpkg: warning: package not in database at line 1: g++-4.8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method + for VERSION in '$VERSIONS' + rm -f g++-4.9 gcc-4.9 cpp-4.9 + ln -s clang++ g++-4.9 + ln -s clang gcc-4.9 + ln -s clang cpp-4.9 + echo 'gcc-4.9 hold' + dpkg --set-selections + echo 'g++-4.9 hold' + dpkg --set-selections + cd - /«BUILDDIR» + echo 'Check if gcc, g++ & cpp are actually clang' Check if gcc, g++ & cpp are actually clang + gcc --version + grep clang + cpp --version + grep clang + g++ --version + grep clang I: Finished running '/tmp/switch-to-clang'. Finished processing commands. ──────────────────────────────────────────────────────────────────────────────── Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-Aod0Pg/apt_archive/sbuild-build-depends-core-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install core build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy debconf: delaying package configuration, since apt-utils is not installed 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 0 B/816 B of archives. After this operation, 0 B of additional disk space will be used. Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 14431 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8.0.0), libffindex0-dev (>= 0.9.6.1), help2man, libpng12-dev Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8.0.0), libffindex0-dev (>= 0.9.6.1), help2man, libpng12-dev dpkg-deb: building package `sbuild-build-depends-hhsuite-dummy' in `/«BUILDDIR»/resolver-8rg8GF/apt_archive/sbuild-build-depends-hhsuite-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install hhsuite build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: bsdmainutils debhelper file gettext gettext-base groff-base help2man intltool-debian libasprintf0c2 libcroco3 libffindex0 libffindex0-dev libglib2.0-0 libmagic1 libpipeline1 libpng12-0 libpng12-dev libunistring0 libxml2 man-db po-debconf zlib1g-dev Suggested packages: wamerican wordlist whois vacation dh-make gettext-doc groff less www-browser libmail-box-perl Recommended packages: curl wget lynx-cur autopoint libasprintf-dev libgettextpo-dev libglib2.0-data shared-mime-info xml-core libmail-sendmail-perl The following NEW packages will be installed: bsdmainutils debhelper file gettext gettext-base groff-base help2man intltool-debian libasprintf0c2 libcroco3 libffindex0 libffindex0-dev libglib2.0-0 libmagic1 libpipeline1 libpng12-0 libpng12-dev libunistring0 libxml2 man-db po-debconf sbuild-build-depends-hhsuite-dummy zlib1g-dev 0 upgraded, 23 newly installed, 0 to remove and 0 not upgraded. Need to get 9421 kB/9422 kB of archives. After this operation, 28.1 MB of additional disk space will be used. Get:1 http://localhost:9999/debian/ unstable/main libpipeline1 amd64 1.3.0-1 [25.8 kB] Get:2 http://localhost:9999/debian/ unstable/main groff-base amd64 1.22.2-5 [1043 kB] Get:3 http://localhost:9999/debian/ unstable/main bsdmainutils amd64 9.0.5 [211 kB] Get:4 http://localhost:9999/debian/ unstable/main man-db amd64 2.6.7.1-1 [990 kB] Get:5 http://localhost:9999/debian/ unstable/main libasprintf0c2 amd64 0.18.3.2-2 [29.4 kB] Get:6 http://localhost:9999/debian/ unstable/main libmagic1 amd64 1:5.19-1 [237 kB] Get:7 http://localhost:9999/debian/ unstable/main libxml2 amd64 2.9.1+dfsg1-3 [791 kB] Get:8 http://localhost:9999/debian/ unstable/main libglib2.0-0 amd64 2.40.0-3 [2405 kB] Get:9 http://localhost:9999/debian/ unstable/main libcroco3 amd64 0.6.8-2 [133 kB] Get:10 http://localhost:9999/debian/ unstable/main libpng12-0 amd64 1.2.50-1 [189 kB] Get:11 http://localhost:9999/debian/ unstable/main libunistring0 amd64 0.9.3-5 [434 kB] Get:12 http://localhost:9999/debian/ unstable/main file amd64 1:5.19-1 [58.0 kB] Get:13 http://localhost:9999/debian/ unstable/main gettext-base amd64 0.18.3.2-2 [116 kB] Get:14 http://localhost:9999/debian/ unstable/main gettext amd64 0.18.3.2-2 [1202 kB] Get:15 http://localhost:9999/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB] Get:16 http://localhost:9999/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB] Get:17 http://localhost:9999/debian/ unstable/main debhelper all 9.20140613 [692 kB] Get:18 http://localhost:9999/debian/ unstable/main help2man amd64 1.45.1 [95.9 kB] Get:19 http://localhost:9999/debian/ unstable/main zlib1g-dev amd64 1:1.2.8.dfsg-1 [217 kB] Get:20 http://localhost:9999/debian/ unstable/main libpng12-dev amd64 1.2.50-1 [267 kB] Get:21 http://localhost:9999/debian/ unstable/main libffindex0 amd64 0.9.9.3-1 [15.5 kB] Get:22 http://localhost:9999/debian/ unstable/main libffindex0-dev amd64 0.9.9.3-1 [15.4 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 9421 kB in 1s (8553 kB/s) Selecting previously unselected package libpipeline1:amd64. (Reading database ... 14431 files and directories currently installed.) Preparing to unpack .../libpipeline1_1.3.0-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.3.0-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../groff-base_1.22.2-5_amd64.deb ... Unpacking groff-base (1.22.2-5) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../bsdmainutils_9.0.5_amd64.deb ... Unpacking bsdmainutils (9.0.5) ... Selecting previously unselected package man-db. Preparing to unpack .../man-db_2.6.7.1-1_amd64.deb ... Unpacking man-db (2.6.7.1-1) ... Selecting previously unselected package libasprintf0c2:amd64. Preparing to unpack .../libasprintf0c2_0.18.3.2-2_amd64.deb ... Unpacking libasprintf0c2:amd64 (0.18.3.2-2) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../libmagic1_1%3a5.19-1_amd64.deb ... Unpacking libmagic1:amd64 (1:5.19-1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../libxml2_2.9.1+dfsg1-3_amd64.deb ... Unpacking libxml2:amd64 (2.9.1+dfsg1-3) ... Selecting previously unselected package libglib2.0-0:amd64. Preparing to unpack .../libglib2.0-0_2.40.0-3_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.40.0-3) ... Selecting previously unselected package libcroco3:amd64. Preparing to unpack .../libcroco3_0.6.8-2_amd64.deb ... Unpacking libcroco3:amd64 (0.6.8-2) ... Selecting previously unselected package libpng12-0:amd64. Preparing to unpack .../libpng12-0_1.2.50-1_amd64.deb ... Unpacking libpng12-0:amd64 (1.2.50-1) ... Selecting previously unselected package libunistring0:amd64. Preparing to unpack .../libunistring0_0.9.3-5_amd64.deb ... Unpacking libunistring0:amd64 (0.9.3-5) ... Selecting previously unselected package file. Preparing to unpack .../file_1%3a5.19-1_amd64.deb ... Unpacking file (1:5.19-1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../gettext-base_0.18.3.2-2_amd64.deb ... Unpacking gettext-base (0.18.3.2-2) ... Selecting previously unselected package gettext. Preparing to unpack .../gettext_0.18.3.2-2_amd64.deb ... Unpacking gettext (0.18.3.2-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../intltool-debian_0.35.0+20060710.1_all.deb ... Unpacking intltool-debian (0.35.0+20060710.1) ... Selecting previously unselected package po-debconf. Preparing to unpack .../po-debconf_1.0.16+nmu2_all.deb ... Unpacking po-debconf (1.0.16+nmu2) ... Selecting previously unselected package debhelper. Preparing to unpack .../debhelper_9.20140613_all.deb ... Unpacking debhelper (9.20140613) ... Selecting previously unselected package help2man. Preparing to unpack .../help2man_1.45.1_amd64.deb ... Unpacking help2man (1.45.1) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../zlib1g-dev_1%3a1.2.8.dfsg-1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.2.8.dfsg-1) ... Selecting previously unselected package libpng12-dev. Preparing to unpack .../libpng12-dev_1.2.50-1_amd64.deb ... Unpacking libpng12-dev (1.2.50-1) ... Selecting previously unselected package libffindex0. Preparing to unpack .../libffindex0_0.9.9.3-1_amd64.deb ... Unpacking libffindex0 (0.9.9.3-1) ... Selecting previously unselected package libffindex0-dev. Preparing to unpack .../libffindex0-dev_0.9.9.3-1_amd64.deb ... Unpacking libffindex0-dev (0.9.9.3-1) ... Selecting previously unselected package sbuild-build-depends-hhsuite-dummy. Preparing to unpack .../sbuild-build-depends-hhsuite-dummy.deb ... Unpacking sbuild-build-depends-hhsuite-dummy (0.invalid.0) ... Setting up libpipeline1:amd64 (1.3.0-1) ... Setting up groff-base (1.22.2-5) ... Setting up bsdmainutils (9.0.5) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up man-db (2.6.7.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libasprintf0c2:amd64 (0.18.3.2-2) ... Setting up libmagic1:amd64 (1:5.19-1) ... Setting up libxml2:amd64 (2.9.1+dfsg1-3) ... Setting up libglib2.0-0:amd64 (2.40.0-3) ... No schema files found: doing nothing. Setting up libcroco3:amd64 (0.6.8-2) ... Setting up libpng12-0:amd64 (1.2.50-1) ... Setting up libunistring0:amd64 (0.9.3-5) ... Setting up file (1:5.19-1) ... Setting up gettext-base (0.18.3.2-2) ... Setting up gettext (0.18.3.2-2) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu2) ... Setting up debhelper (9.20140613) ... Setting up help2man (1.45.1) ... Setting up zlib1g-dev:amd64 (1:1.2.8.dfsg-1) ... Setting up libpng12-dev (1.2.50-1) ... Setting up libffindex0 (0.9.9.3-1) ... Setting up libffindex0-dev (0.9.9.3-1) ... Setting up sbuild-build-depends-hhsuite-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.19-2) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 2.6.32-5-xen-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.24.51.20140604-3 dpkg-dev_1.17.10 g++-4.6_4.6.4-7 g++-4.9_4.9.0-6 gcc-4.6_4.6.4-7 gcc-4.7_4.7.4-1 gcc-4.9_4.9.0-6 libc6-dev_2.19-2 libstdc++-4.9-dev_4.9.0-6 libstdc++6_4.9.0-6 libstdc++6-4.6-dev_4.6.4-7 linux-libc-dev_3.14.7-1 Package versions: apt_1.0.4 base-files_7.3 base-passwd_3.5.33 bash_4.3-7 binutils_2.24.51.20140604-3 bsdmainutils_9.0.5 bsdutils_1:2.20.1-5.8 build-essential_11.6 bzip2_1.0.6-5 clang-3.4_1:3.4.2-2 coreutils_8.21-1.2 cpp_4:4.9.0-3 cpp-4.6_4.6.4-7 cpp-4.7_4.7.4-1 cpp-4.9_4.9.0-6 dash_0.5.7-4 debconf_1.5.53 debconf-i18n_1.5.53 debfoster_2.7-1.2 debhelper_9.20140613 debian-archive-keyring_2012.4 debianutils_4.4 diffutils_1:3.3-1 dpkg_1.17.10 dpkg-dev_1.17.10 e2fslibs_1.42.10-1 e2fsprogs_1.42.10-1 fakeroot_1.20-3 file_1:5.19-1 findutils_4.4.2-8 g++_4:4.9.0-3 g++-4.6_4.6.4-7 g++-4.9_4.9.0-6 gcc_4:4.9.0-3 gcc-4.4-base_4.4.7-8 gcc-4.5-base_4.5.4-1 gcc-4.6_4.6.4-7 gcc-4.6-base_4.6.4-7 gcc-4.7_4.7.4-1 gcc-4.7-base_4.7.4-1 gcc-4.8-base_4.8.3-3 gcc-4.9_4.9.0-6 gcc-4.9-base_4.9.0-6 gettext_0.18.3.2-2 gettext-base_0.18.3.2-2 gnupg_1.4.16-1.1 gpgv_1.4.16-1.1 grep_2.18-2 groff-base_1.22.2-5 gzip_1.6-3 help2man_1.45.1 hostname_3.15 initscripts_2.88dsf-53.2 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 libacl1_2.2.52-1 libapt-pkg4.12_1.0.4 libarchive-extract-perl_0.72-1 libasan1_4.9.0-6 libasprintf0c2_0.18.3.2-2 libatomic1_4.9.0-6 libattr1_1:2.4.47-1 libaudit-common_1:2.3.7-1 libaudit1_1:2.3.7-1 libblkid1_2.20.1-5.8 libbz2-1.0_1.0.6-5 libc-bin_2.19-2 libc-dev-bin_2.19-2 libc6_2.19-2 libc6-dev_2.19-2 libcap2_1:2.22-1.2 libcilkrts5_4.9.0-6 libclang-common-3.4-dev_1:3.4.2-2 libclang1-3.4_1:3.4.2-2 libclass-isa-perl_0.36-5 libcloog-isl4_0.18.2-1 libcloog-ppl1_0.16.1-5 libcomerr2_1.42.10-1 libcroco3_0.6.8-2 libdb5.1_5.1.29-5 libdb5.3_5.3.28-3 libdebconfclient0_0.191 libdpkg-perl_1.17.10 libfakeroot_1.20-3 libffi6_3.1-2 libffindex0_0.9.9.3-1 libffindex0-dev_0.9.9.3-1 libfile-fcntllock-perl_0.20-1 libgc1c2_1:7.2d-6 libgcc-4.7-dev_4.7.4-1 libgcc-4.9-dev_4.9.0-6 libgcc1_1:4.9.0-6 libgdbm3_1.8.3-12 libglib2.0-0_2.40.0-3 libgmp10_2:6.0.0+dfsg-4 libgmpxx4ldbl_2:6.0.0+dfsg-4 libgomp1_4.9.0-6 libgpm2_1.20.4-6.1 libisl10_0.12.2-1 libitm1_4.9.0-6 libllvm3.4_1:3.4.2-2 liblocale-gettext-perl_1.05-8 liblog-message-simple-perl_0.10-1 liblsan0_4.9.0-6 liblzma5_5.1.1alpha+20120614-2 libmagic1_1:5.19-1 libmodule-pluggable-perl_5.1-1 libmount1_2.20.1-5.8 libmpc2_0.9-4 libmpc3_1.0.1-1 libmpfr4_3.1.2-1 libncurses5_5.9+20140118-1 libobjc-4.9-dev_4.9.0-6 libobjc4_4.9.0-6 libpam-modules_1.1.8-3 libpam-modules-bin_1.1.8-3 libpam-runtime_1.1.8-3 libpam0g_1.1.8-3 libpcre3_1:8.31-5 libpipeline1_1.3.0-1 libpng12-0_1.2.50-1 libpng12-dev_1.2.50-1 libpod-latex-perl_0.61-1 libppl-c4_1:1.1-2+b1 libppl13_1:1.1-2+b1 libquadmath0_4.9.0-6 libreadline6_6.3-6 libselinux1_2.3-1 libsemanage-common_2.3-1 libsemanage1_2.3-1 libsepol1_2.3-1 libslang2_2.2.4-16 libss2_1.42.10-1 libstdc++-4.9-dev_4.9.0-6 libstdc++6_4.9.0-6 libstdc++6-4.6-dev_4.6.4-7 libswitch-perl_2.17-1 libterm-ui-perl_0.42-1 libtext-charwidth-perl_0.04-7+b2 libtext-iconv-perl_1.7-5+b1 libtext-soundex-perl_3.4-1+b1 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_2.3000-2 libtinfo5_5.9+20140118-1 libtsan0_4.9.0-6 libubsan0_4.9.0-6 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23.3 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.8 libvtv0_4.9.0-6 libxml2_2.9.1+dfsg1-3 linux-libc-dev_3.14.7-1 login_1:4.2-2 lsb-base_4.1+Debian13 make_4.0-8 man-db_2.6.7.1-1 mawk_1.3.3-17 mount_2.20.1-5.8 multiarch-support_2.19-2 ncurses-base_5.9+20140118-1 ncurses-bin_5.9+20140118-1 passwd_1:4.2-2 patch_2.7.1-5 perl_5.18.2-4 perl-base_5.18.2-4 perl-modules_5.18.2-4 po-debconf_1.0.16+nmu2 readline-common_6.3-6 rename_0.20-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-hhsuite-dummy_0.invalid.0 sed_4.2.2-4 sensible-utils_0.0.9 startpar_0.59-3 sudo_1.8.9p5-1 sysv-rc_2.88dsf-53.2 sysvinit_2.88dsf-53.2 sysvinit-core_2.88dsf-53.2 sysvinit-utils_2.88dsf-53.2 tar_1.27.1-2 tzdata_2014e-1 ucf_3.0030 util-linux_2.20.1-5.8 vim_2:7.4.273-2+b1 vim-common_2:7.4.273-2+b1 vim-runtime_2:7.4.273-2 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.8.dfsg-1 zlib1g-dev_1:1.2.8.dfsg-1 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error gpgv: Signature made Thu May 23 12:14:09 2013 UTC using RSA key ID 9A0C52FA gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./hhsuite_2.0.16-1.dsc dpkg-source: info: extracting hhsuite in hhsuite-2.0.16 dpkg-source: info: unpacking hhsuite_2.0.16.orig.tar.gz dpkg-source: info: unpacking hhsuite_2.0.16-1.debian.tar.gz dpkg-source: info: applying Makefile dpkg-source: info: applying paths dpkg-source: info: applying help dpkg-source: info: applying rest1 dpkg-source: info: applying perlscript_uselib dpkg-source: info: applying hardening dpkg-source: info: applying unused_variables_warning dpkg-source: info: applying unnecessary_libz dpkg-source: info: applying perl_interpreter dpkg-source: info: applying version_bump Check disc space ──────────────── Sufficient free space for build Hack binNMU version ─────────────────── Created changelog entry for binNMU version 2.0.16-1clang1 User Environment ──────────────── DEB_BUILD_OPTIONS=parallel=10 HOME=/sbuild-nonexistent LOGNAME=user PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=unstable-amd64-sbuild SCHROOT_CHROOT_NAME=unstable-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1000 SCHROOT_GROUP=user SCHROOT_SESSION_ID=unstable-amd64-sbuild-296c1dd7-b3a3-419b-97de-8888214a3548 SCHROOT_UID=1000 SCHROOT_USER=user SHELL=/bin/sh USER=user dpkg-buildpackage ───────────────── dpkg-buildpackage: source package hhsuite dpkg-buildpackage: source version 2.0.16-1clang1 dpkg-buildpackage: source distribution unstable dpkg-source --before-build hhsuite-2.0.16 dpkg-buildpackage: host architecture amd64 dpkg-source: warning: unknown information field 'Dm-Upload-Allowed' in input data in general section of control info file fakeroot debian/rules clean dh clean --parallel dh_testdir -O--parallel dh_auto_clean -O--parallel make[1]: Entering directory '/«PKGBUILDDIR»' make -C src clean make[2]: Entering directory '/«PKGBUILDDIR»/src' rm -f *.o cs/*.o rm -f hhconsensus hhconsensus_valgrind hhfilter_valgrind hhfilter hhalign_valgrind hhalign hhmake hhblits_valgrind hhblits hhsearch_valgrind hhsearch cstranslate make[2]: Leaving directory '/«PKGBUILDDIR»/src' make[1]: Leaving directory '/«PKGBUILDDIR»' debian/rules override_dh_clean make[1]: Entering directory '/«PKGBUILDDIR»' rm -f hhalign.1 hhblits.1 hhconsensus.1 hhfilter.1 hhmake.1 hhsearch.1 dh_clean make[1]: Leaving directory '/«PKGBUILDDIR»' debian/rules build-arch dh build-arch --parallel dh_testdir -a -O--parallel dh_auto_configure -a -O--parallel dh_auto_build -a -O--parallel make[1]: Entering directory '/«PKGBUILDDIR»' make -C data all make[2]: Entering directory '/«PKGBUILDDIR»/data' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/«PKGBUILDDIR»/data' make -C src all make[2]: Entering directory '/«PKGBUILDDIR»/src' g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics -fopenmp -DHH_SSE3 -msse3 -Wl,-z,relro -fopenmp -c cs/blosum_matrix.cc -o cs/blosum_matrix.o g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics -fopenmp -DHH_SSE3 -msse3 -Wl,-z,relro -fopenmp -c cs/as.cc -o cs/as.o g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics -fopenmp -DHH_SSE3 -msse3 -Wl,-z,relro -fopenmp -c cs/log.cc -o cs/log.o g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics -fopenmp -DHH_SSE3 -msse3 -Wl,-z,relro -fopenmp -c cs/application.cc -o cs/application.o g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics -fopenmp -DHH_SSE3 -msse3 -Wl,-z,relro -fopenmp -c cs/getopt_pp.cc -o cs/getopt_pp.o g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics -fopenmp -DHH_SSE3 -msse3 -Wl,-z,relro -fopenmp -c cs/assert_helpers.cc -o cs/assert_helpers.o g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics -fopenmp -DHH_SSE3 -msse3 -Wl,-z,relro -fopenmp -c cs/aa.cc -o cs/aa.o clang: warning: -Wl,-z,relro: 'linker' input unused clangclang: warning: -Wl,-z,relro: 'linker' input unused clang: warning: argument unused during compilation: '-fopenmp' clang: warning: argument unused during compilation: '-fopenmp' clangclang: warning: -Wl,-z,relro: 'linker' input unused clang: warning: -Wl,-z,relro: 'linker' input unused : warning: -Wl,-z,relro: 'linker' input unused clang: warning: argument unused during compilation: '-fopenmp' clang: warning: argument unused during compilation: '-fopenmp' clang: warning: argument unused during compilation: '-fopenmp' clang: warning: argument unused during compilation: '-fopenmp' clang: warning: -Wl,-z,relro: 'linker' input unused clang: warning: argument unused during compilation: '-fopenmp' clang: warning: argument unused during compilation: '-fopenmp' clang: warning: argument unused during compilation: '-fopenmp' clang: warning: argument unused during compilation: '-fopenmp' : warning: argument unused during compilation: '-fopenmp' clang: warning: argument unused during compilation: '-fopenmp' clang: warning: -Wl,-z,relro: 'linker' input unused clang: warning: argument unused during compilation: '-fopenmp' clang: warning: argument unused during compilation: '-fopenmp' g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics -fopenmp -DHH_SSE3 -msse3 -Wl,-z,relro hhblits.C -o hhblits cs/blosum_matrix.o cs/as.o cs/log.o cs/application.o cs/getopt_pp.o cs/assert_helpers.o cs/aa.o -lpthread -fopenmp -lrt -lffindex g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics -fopenmp -DHH_SSE3 -msse3 -Wl,-z,relro hhsearch.C -o hhsearch cs/blosum_matrix.o cs/as.o cs/log.o cs/application.o cs/getopt_pp.o cs/assert_helpers.o cs/aa.o -lpthread -lrt g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics -fopenmp -DHH_SSE3 -msse3 -Wl,-z,relro hhmake.C -o hhmake cs/blosum_matrix.o cs/as.o cs/log.o cs/application.o cs/getopt_pp.o cs/assert_helpers.o cs/aa.o g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics -fopenmp -DHH_SSE3 -msse3 -Wl,-z,relro hhalign.C -o hhalign cs/blosum_matrix.o cs/as.o cs/log.o cs/application.o cs/getopt_pp.o cs/assert_helpers.o cs/aa.o -DNO_FREETYPE -DHH_PNG -lpng g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics -fopenmp -DHH_SSE3 -msse3 -Wl,-z,relro hhfilter.C -o hhfilter cs/blosum_matrix.o cs/as.o cs/log.o cs/application.o cs/getopt_pp.o cs/assert_helpers.o cs/aa.o g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics -fopenmp -DHH_SSE3 -msse3 -Wl,-z,relro hhconsensus.C -o hhconsensus cs/blosum_matrix.o cs/as.o cs/log.o cs/application.o cs/getopt_pp.o cs/assert_helpers.o cs/aa.o g++ -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics -fopenmp -DHH_SSE3 -msse3 -Wl,-z,relro -lm -o cstranslate cs/cstranslate_app.cc cs/blosum_matrix.o cs/as.o cs/log.o cs/application.o cs/getopt_pp.o cs/assert_helpers.o cs/aa.o In file included from In file included from hhalign.C:78: In file included from cs/context_library.h:8: In file included from cs/context_profile.h:7: In file included from cs/count_profile-inl.h:6: In file included from cs/count_profile.h:6: cs/alignment.h:93:56: error: reference to non-static member function must be called cs/cstranslate_app.cc:4: In file included from cs/alignment-inl.h:6: cs/alignment.h:93:56: error: reference to non-static member function must be called void set_name(const std::string& header) { name_ = name; } ^~~~ void set_name(const std::string& header) { name_ = name; } ^~~~ In file included from hhfilter.C:66: In file included from cs/context_library.h:8: In file included from cs/context_profile.h:7: In file included from cs/count_profile-inl.h:6: In file included from cs/count_profile.h:6: cs/alignment.h:93:56: error: reference to non-static member function must be called void set_name(const std::string& header) { name_ = name; } ^~~~ In file included from hhblits.C:123: In file included from cs/context_library.h:8: In file included from cs/context_profile.h:7: In file included from cs/count_profile-inl.h:6: In file included from cs/count_profile.h:6: cs/alignment.h:93:56: error: reference to non-static member function must be called void set_name(const std::string& header) { name_ = name; } ^~~~ In file included from hhmake.C:66: In file included from cs/context_library.h:8: In file included from cs/context_profile.h:7: In file included from cs/count_profile-inl.h:6: In file included from cs/count_profile.h:6: cs/alignment.h:93:56: error: reference to non-static member function must be called void set_name(const std::string& header) { name_ = name; } ^~~~ In file included from cs/cstranslate_app.cc:4: cs/alignment-inl.h:655:15: warning: comparison of constant -1 with expression of type 'uint8_t' (aka 'unsigned char') is always false [-Wtautological-constant-out-of-range-compare] if (c == EOF) break; ~ ^ ~~~ In file included from hhsearch.C:93: In file included from cs/context_library.h:8: In file included from cs/context_profile.h:7: In file included from cs/count_profile-inl.h:6: In file included from cs/count_profile.h:6: cs/alignment.h:93:56: error: reference to non-static member function must be called void set_name(const std::string& header) { name_ = name; } ^~~~ cs/alignment-inl.h:827:21: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ In file included from hhalign.C:78: In file included from cs/context_library.h:8: In file included from cs/context_profile.h:7: In file included from cs/count_profile-inl.h:8: cs/alignment-inl.h:655:15: warning: comparison of constant -1 with expression of type 'uint8_t' (aka 'unsigned char') is always false [-Wtautological-constant-out-of-range-compare] if (c == EOF) break; ~ ^ ~~~ cs/alignment-inl.h:827:21: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ In file included from hhfilter.C:66: In file included from cs/context_library.h:8: In file included from cs/context_profile.h:7: In file included from cs/count_profile-inl.h:8: cs/alignment-inl.h:655:15: warning: comparison of constant -1 with expression of type 'uint8_t' (aka 'unsigned char') is always false [-Wtautological-constant-out-of-range-compare] if (c == EOF) break; ~ ^ ~~~ In file included from hhblits.C:123: In file included from cs/context_library.h:8: In file included from cs/context_profile.h:7: In file included from cs/count_profile-inl.h:8: cs/alignment-inl.h:655:15: warning: comparison of constant -1 with expression of type 'uint8_t' (aka 'unsigned char') is always false [-Wtautological-constant-out-of-range-compare] if (c == EOF) break; ~ ^ ~~~ In file included from hhmake.C:66: In file included from cs/context_library.h:8: In file included from cs/context_profile.h:7: In file included from cs/count_profile-inl.h:8: cs/alignment-inl.h:655:15: warning: comparison of constant -1 with expression of type 'uint8_t' (aka 'unsigned char') is always false [-Wtautological-constant-out-of-range-compare] if (c == EOF) break; ~ ^ ~~~ In file included from hhalign.C:78: In file included from cs/context_library.h:9: cs/pseudocounts.h:14:1: warning: class template 'CountProfile' was previously declared as a struct template [-Wmismatched-tags] class CountProfile; ^ cs/count_profile.h:14:8: note: previous use is here struct CountProfile { ^ cs/pseudocounts.h:14:1: note: did you mean struct here? class CountProfile; ^~~~~ struct cs/alignment-inl.hcs/alignment-inl.h:827:21: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ cs/alignment-inl.h:827:21: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ :827:21: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ In file included from hhsearch.C:93: In file included from cs/context_library.h:8: In file included from cs/context_profile.h:7: In file included from cs/count_profile-inl.h:8: cs/alignment-inl.h:655:15: warning: comparison of constant -1 with expression of type 'uint8_t' (aka 'unsigned char') is always false [-Wtautological-constant-out-of-range-compare] if (c == EOF) break; ~ ^ ~~~ In file included from hhblits.C:123: In file included from cs/context_library.h:9: cs/pseudocounts.h:14:1: warning: class template 'CountProfile' was previously declared as a struct template [-Wmismatched-tags] class CountProfile; ^ cs/count_profile.h:14:8: note: previous use is here struct CountProfile { ^ cs/pseudocounts.h:14:1: note: did you mean struct here? class CountProfile; ^~~~~ struct In file included from hhconsensus.C:52: In file included from cs/context_library.h:8: In file included from cs/context_profile.h:7: In file included from cs/count_profile-inl.h:6: In file included from cs/count_profile.h:6: cs/alignment.h:93:56: error: reference to non-static member function must be called void set_name(const std::string& header) { name_ = name; } ^~~~ cs/alignment-inl.hIn file included from hhmake.C:66: In file included from cs/context_library.h:9: cs/pseudocounts.h:14:1: warning: class template 'CountProfile' was previously declared as a struct template [-Wmismatched-tags] class CountProfile; ^ cs/count_profile.h:14:8: note: previous use is here struct CountProfile { ^ cs/pseudocounts.h:14:1: note: did you mean struct here? class CountProfile; ^~~~~ struct In file included from :827:21: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ hhfilter.C:66: In file included from cs/context_library.h:9: cs/pseudocounts.h:14:1: warning: class template 'CountProfile' was previously declared as a struct template [-Wmismatched-tags] class CountProfile; ^ cs/count_profile.h:14:8: note: previous use is here struct CountProfile { ^ cs/pseudocounts.h:14:1: note: did you mean struct here? class CountProfile; ^~~~~ struct In file included from hhsearch.C:93: In file included from cs/context_library.h:9: cs/pseudocounts.h:14:1: warning: class template 'CountProfile' was previously declared as a struct template [-Wmismatched-tags] class CountProfile; ^ cs/count_profile.h:14:8: note: previous use is here struct CountProfile { ^ In file included from cs/cstranslate_app.cc:7: In file included from cs/context_library.h:9: cs/pseudocounts.h:14:1: warning: class template 'CountProfile' was previously declared as a struct template [-Wmismatched-tags] class CountProfile; ^ cs/count_profile.h:14:8: note: previous use is here struct CountProfile { ^ cs/pseudocounts.h:14:1: note: did you mean struct here? class CountProfile; ^~~~~ struct cs/pseudocounts.h:14:1: note: did you mean struct here? class CountProfile; ^~~~~ struct In file included from hhconsensus.C:52: In file included from cs/context_library.h:8: In file included from cs/context_profile.h:7: In file included from cs/count_profile-inl.h:8: cs/alignment-inl.h:655:15: warning: comparison of constant -1 with expression of type 'uint8_t' (aka 'unsigned char') is always false [-Wtautological-constant-out-of-range-compare] if (c == EOF) break; ~ ^ ~~~ cs/alignment-inl.h:827:21: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ In file included from hhconsensus.C:52: In file included from cs/context_library.h:9: cs/pseudocounts.h:14:1: warning: class template 'CountProfile' was previously declared as a struct template [-Wmismatched-tags] class CountProfile; ^ cs/count_profile.h:14:8: note: previous use is here struct CountProfile { ^ cs/pseudocounts.h:14:1: note: did you mean struct here? class CountProfile; ^~~~~ struct In file included from hhalign.C:85: ./hhutil.C:478:49: warning: when type is in parentheses, array cannot have dynamic size argv_conf[argc_conf]=new(char[strlen(c_first)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhutil.C:483:45: warning: when type is in parentheses, array cannot have dynamic size argv_conf[argc_conf]=new(char[strlen(c_first)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ In file included from hhfilter.C:74: ./hhutil.C:478:49: warning: when type is in parentheses, array cannot have dynamic size argv_conf[argc_conf]=new(char[strlen(c_first)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhutil.C:483:45: warning: when type is in parentheses, array cannot have dynamic size argv_conf[argc_conf]=new(char[strlen(c_first)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ In file included from hhmake.C:74: ./hhutil.C:478:49: warning: when type is in parentheses, array cannot have dynamic size argv_conf[argc_conf]=new(char[strlen(c_first)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhutil.C:483:45: warning: when type is in parentheses, array cannot have dynamic size argv_conf[argc_conf]=new(char[strlen(c_first)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ In file included from hhblits.C:132: ./hhutil.C:478:49: warning: when type is in parentheses, array cannot have dynamic size argv_conf[argc_conf]=new(char[strlen(c_first)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhutil.C:483:45: warning: when type is in parentheses, array cannot have dynamic size argv_conf[argc_conf]=new(char[strlen(c_first)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ In file included from hhsearch.C:102: ./hhutil.C:478:49: warning: when type is in parentheses, array cannot have dynamic size argv_conf[argc_conf]=new(char[strlen(c_first)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhutil.C:483:45: warning: when type is in parentheses, array cannot have dynamic size argv_conf[argc_conf]=new(char[strlen(c_first)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ In file included from hhalign.C:95: ./hhhmm.C:169:23: warning: when type is in parentheses, array cannot have dynamic size sname[k]=new(char[strlen(q.sname[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:174:21: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(q.seq[k])+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ In file included from hhfilter.C:81: ./hhhmm.C:169:23: warning: when type is in parentheses, array cannot have dynamic size sname[k]=new(char[strlen(q.sname[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:174:21: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(q.seq[k])+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhhmm.CIn file included from hhmake.C:81: ./hhhmm.C:169:23: warning: when type is in parentheses, array cannot have dynamic size sname[k]=new(char[strlen(q.sname[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ :360:39: warning: ./hhhmm.Cwhen type is in parentheses, array cannot have dynamic size:174:21: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(q.seq[k])+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ seq[k-1]=new(char[strlen(cur_seq)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:367:40: warning: when type is in parentheses, array cannot have dynamic size sname[k] = new (char[strlen(line+1)+1]); //+1 for terminating '\0' ~ ^~~~~~~~~~~~~~~~ ~ ./hhhmm.C:360:39: warning: when type is in parentheses, array cannot have dynamic size seq[k-1]=new(char[strlen(cur_seq)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:367:40: warning: when type is in parentheses, array cannot have dynamic size sname[k] = new (char[strlen(line+1)+1]); //+1 for terminating '\0' ~ ^~~~~~~~~~~~~~~~ ~ ./hhhmm.C:360:39: warning: when type is in parentheses, array cannot have dynamic size seq[k-1]=new(char[strlen(cur_seq)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:367:40: warning: when type is in parentheses, array cannot have dynamic size sname[k] = new (char[strlen(line+1)+1]); //+1 for terminating '\0' ~ ^~~~~~~~~~~~~~~~ ~ ./hhhmm.C:468:29: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(cur_seq)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:468:29: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(cur_seq)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ In file included from hhblits.C:142: ./hhhmm.C:169:23: warning: when type is in parentheses, array cannot have dynamic size sname[k]=new(char[strlen(q.sname[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:174:21: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(q.seq[k])+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ In file included from hhsearch.C:112: ./hhhmm.C:169:23: warning: when type is in parentheses, array cannot have dynamic size sname[k]=new(char[strlen(q.sname[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:174:21: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(q.seq[k])+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C3./hhhmm.C:360:39: warning: when type is in parentheses, array cannot have dynamic size seq[k-1]=new(char[strlen(cur_seq)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:468:29: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(cur_seq)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ :367:40: warning: when type is in parentheses, array cannot have dynamic size sname[k] = new (char[strlen(line+1)+1]); //+1 for terminating '\0' ~ ^~~~~~~~~~~~~~~~ ~ ./hhhmm.C:360:39: warning: when type is in parentheses, array cannot have dynamic size seq[k-1]=new(char[strlen(cur_seq)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ warnings and 1 error generated. ./hhhmm.C:367:40: warning: when type is in parentheses, array cannot have dynamic size sname[k] = new (char[strlen(line+1)+1]); //+1 for terminating '\0' ~ ^~~~~~~~~~~~~~~~ ~ ./hhhmm.C:719:40: warning: when type is in parentheses, array cannot have dynamic size seq[nsa_dssp] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C:740:40: warning: when type is in parentheses, array cannot have dynamic size seq[nss_pred] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C:761:40: warning: when type is in parentheses, array cannot have dynamic size seq[nss_conf] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ Makefile:80: recipe for target 'cstranslate' failed make[2]: *** [cstranslate] Error 1 make[2]: *** Waiting for unfinished jobs.... ./hhhmm.C:719:40: warning: when type is in parentheses, array cannot have dynamic size seq[nsa_dssp] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C:740:40: warning: when type is in parentheses, array cannot have dynamic size seq[nss_pred] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C:761:40: warning: when type is in parentheses, array cannot have dynamic size seq[nss_conf] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C:468:29: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(cur_seq)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:835:36: warning: when type is in parentheses, array cannot have dynamic size seq[nss_dssp] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.CIn file included from hhconsensus.C:60: ./hhutil.C:478:49: warning: when type is in parentheses, array cannot have dynamic size argv_conf[argc_conf]=new(char[strlen(c_first)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhutil.C:483:45: warning: when type is in parentheses, array cannot have dynamic size argv_conf[argc_conf]=new(char[strlen(c_first)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:835:36: warning: when type is in parentheses, array cannot have dynamic size seq[nss_dssp] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ :719:40: warning: when type is in parentheses, array cannot have dynamic size seq[nsa_dssp] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C:740:40: warning: when type is in parentheses, array cannot have dynamic size seq[nss_pred] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C:761:40: warning: when type is in parentheses, array cannot have dynamic size seq[nss_conf] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C:835:36: warning: when type is in parentheses, array cannot have dynamic size seq[nss_dssp] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C:468:29: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(cur_seq)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhhmm.C./hhhmm.C:719:40: warning: when type is in parentheses, array cannot have dynamic size seq[nsa_dssp] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C:740:40: warning: when type is in parentheses, array cannot have dynamic size seq[nss_pred] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C./hhhmm.C:1009:27: warning: when type is in parentheses, array cannot have dynamic size sname[k+1]=new(char[strlen(longname)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C::1011:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[L+2]); ~ ^~~ ~ 761./hhhmm.C:1014:25: warning: when type is in parentheses, array cannot have dynamic size seq[k+1]=new(char[L+2]); ~ ^~~ ~ :40: warning: when type is in parentheses, array cannot have dynamic size seq[nss_conf] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C:1032:25: warning: when type is in parentheses, array cannot have dynamic size sname[k]=new(char[strlen(longname)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:1034:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[L+2]); ~ ^~~ ~ ./hhhmm.C:1009:27: warning: when type is in parentheses, array cannot have dynamic size sname[k+1]=new(char[strlen(longname)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:1011:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[L+2]); ~ ^~~ ~ :./hhhmm.C835:36: warning: when type is in parentheses, array cannot have dynamic size seq[nss_dssp] = new(char[par.maxres+2]);: 1014 ~ ^~~~~~~~~~~~ ~: 25 :./hhhmm.C:1009:27: warning: when type is in parentheses, array cannot have dynamic size sname[k+1]=new(char[strlen(longname)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C :1011:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[L+2]); ~ ^~~ ~ warning./hhhmm.C:1014:25: warning: when type is in parentheses, array cannot have dynamic size seq[k+1]=new(char[L+2]); ~ ^~~ ~ : when type is in parentheses, array cannot have dynamic size seq[k+1]=new(char[L+2]); ~ ^~~ ~ ./hhhmm.C:1032:25: warning: when type is in parentheses, array cannot have dynamic size sname[k]=new(char[strlen(longname)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:1032:25: warning: when type is in parentheses, array cannot have dynamic size sname[k]=new(char[strlen(longname)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:1034:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[L+2]); ~ ^~~ ~ ./hhhmm.C./hhhmm.C:1034:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[L+2]); ~ ^~~ ~ :1182:40: warning: when type is in parentheses, array cannot have dynamic size seq[nsa_dssp] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C:1203:40: warning: when type is in parentheses, array cannot have dynamic size seq[nss_pred] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C:1224:40: warning: when type is in parentheses, array cannot have dynamic size seq[nss_conf] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C:1182:40: warning: when type is in parentheses, array cannot have dynamic size seq[nsa_dssp] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C:1203:40: warning: when type is in parentheses, array cannot have dynamic size seq[nss_pred] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C:1224:40: warning: when type is in parentheses, array cannot have dynamic size seq[nss_conf] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C./hhhmm.C:1295:36: warning: when type is in parentheses, array cannot have dynamic size seq[nss_dssp] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ :1009:27: warning: when type is in parentheses, array cannot have dynamic size sname[k+1]=new(char[strlen(longname)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:1011:23: warning: when type is in parentheses, array cannot have dynamic size./hhhmm.C: 1182:40: warning: when type is in parentheses, array cannot have dynamic size seq[nsa_dssp] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ seq[k]=new(char[L+2]); ~ ^~~ ~ ./hhhmm.C:1014:25: ./hhhmm.C:1203:40: warning: when type is in parentheses, array cannot have dynamic size seq[nss_pred] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ warning: when type is in parentheses, array cannot have dynamic size seq[k+1]=new(char[L+2]); ~ ^~~ ~ ./hhhmm.C:1224:40: warning: when type is in parentheses, array cannot have dynamic size seq[nss_conf] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C:1032:25: warning: when type is in parentheses, array cannot have dynamic size sname[k]=new(char[strlen(longname)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:1034:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[L+2]); ~ ^~~ ~ ./hhhmm.C:1295:36: warning: when type is in parentheses, array cannot have dynamic size seq[nss_dssp] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C./hhhmm.C:1182:40: warning: when type is in parentheses, array cannot have dynamic size seq[nsa_dssp] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C:1203:40: warning: when type is in parentheses, array cannot have dynamic size ./hhhmm.C:1295:36: warning: when type is in parentheses, array cannot have dynamic size seq[nss_dssp] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ seq[nss_pred] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C:1224:40: warning: when type is in parentheses, array cannot have dynamic size seq[nss_conf] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C:1471:27: warning: when type is in parentheses, array cannot have dynamic size sname[k+1]=new(char[strlen(longname)+1]);:1295:36 : ~ ^~~~~~~~~~~~~~~~~~ ~ warning : when type is in parentheses, array cannot have dynamic size./hhhmm.C seq[nss_dssp] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C:719:40: warning: when type is in parentheses, array cannot have dynamic size seq[nsa_dssp] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ :1473:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[L+2]); ~ ^~~ ~ ./hhhmm.C:740:40: warning: when type is in parentheses, array cannot have dynamic size seq[nss_pred] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C:1476:25: warning: when type is in parentheses, array cannot have dynamic size seq[k+1]=new(char[L+2]); ~ ^~~ ~ ./hhhmm.C:761:40: warning: when type is in parentheses, array cannot have dynamic size seq[nss_conf] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C:1494:25: warning: when type is in parentheses, array cannot have dynamic size sname[k]=new(char[strlen(longname)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:1496:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[L+2]); ~ ^~~ ~ ./hhhmm.C:835:36: warning: when type is in parentheses, array cannot have dynamic size seq[nss_dssp] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C:1471:27: warning: when type is in parentheses, array cannot have dynamic size sname[k+1]=new(char[strlen(longname)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:1473:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[L+2]); ~ ^~~ ~ ./hhhmm.C:1476:25./hhhmm.C:1471:27: warning: when type is in parentheses, array cannot have dynamic size sname[k+1]=new(char[strlen(longname)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ : ./hhhmm.Cwarning:1473:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[L+2]); ~ ^~~ ~ ./hhhmm.C: :1476:25: warning: when type is in parentheses, array cannot have dynamic size seq[k+1]=new(char[L+2]); ~ ^~~ ~ when type is in parentheses, array cannot have dynamic size seq[k+1]=new(char[L+2]); ~ ^~~ ~ ./hhhmm.C:1494:25: warning: when type is in parentheses, array cannot have dynamic size sname[k]=new(char[strlen(longname)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:1496:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[L+2]); ~ ^~~ ~ ./hhhmm.C:1494:25: warning: when type is in parentheses, array cannot have dynamic size sname[k]=new(char[strlen(longname)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:1496:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[L+2]); ~ ^~~ ~ ./hhhmm.C:1471:27: warning: when type is in parentheses, array cannot have dynamic size sname[k+1]=new(char[strlen(longname)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:1473:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[L+2]); ~ ^~~ ~ ./hhhmm.C:1476:25: warning: when type is in parentheses, array cannot have dynamic size seq[k+1]=new(char[L+2]); ~ ^~~ ~ In file included from hhconsensus.C:68: ./hhhmm.C:169:23: warning: when type is in parentheses, array cannot have dynamic size sname[k]=new(char[strlen(q.sname[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:174:21: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(q.seq[k])+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:1494:25: warning: when type is in parentheses, array cannot have dynamic size sname[k]=new(char[strlen(longname)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:1496:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[L+2]); ~ ^~~ ~ ./hhhmm.C:2177:28: warning: when type is in parentheses, array cannot have dynamic size char** lines = new(char*[3*L+100000]); ~ ^~~~~~~~~~ ~ ./hhhmm.C:2205:29: warning: when type is in parentheses, array cannot have dynamic size lines[nline]=new(char[strlen(line)+1]); ~ ^~~~~~~~~~~~~~ ~ ./hhhmm.C./hhhmm.C:1009:27: warning: when type is in parentheses, array cannot have dynamic size sname[k+1]=new(char[strlen(longname)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C::1011:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[L+2]); ~ ^~~ ~ 2329./hhhmm.C:1014:25: warning: when type is in parentheses, array cannot have dynamic size seq[k+1]=new(char[L+2]); ~ ^~~ ~ :30: warning: when type is in parentheses, array cannot have dynamic size seq[nss_pred]=new(char[L+2]); ~ ^~~ ~ ./hhhmm.C:1032:25: warning: when type is in parentheses, array cannot have dynamic size sname[k]=new(char[strlen(longname)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:1034:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[L+2]); ~ ^~~ ~ ./hhhmm.C:2336:30: warning: when type is in parentheses, array cannot have dynamic size seq[nss_conf]=new(char[L+2]); ~ ^~~ ~ In file included from hhmake.C:82: ./hhalignment.C:47:21: warning: when type is in parentheses, array cannot have dynamic size sname = new(char*[maxseq+2]); ~ ^~~~~~~~ ~ ./hhhmm.C:360:39: warning: when type is in parentheses, array cannot have dynamic size seq[k-1]=new(char[strlen(cur_seq)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:367:40: warning: when type is in parentheses, array cannot have dynamic size sname[k] = new (char[strlen(line+1)+1]); //+1 for terminating '\0' ~ ^~~~~~~~~~~~~~~~ ~ ./hhalignment.C:48:19: warning: when type is in parentheses, array cannot have dynamic size seq = new(char*[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:49:15: warning: when type is in parentheses, array cannot have dynamic size l = new(int[maxres]); ~ ^~~~~~ ~ ./hhalignment.C:50:17: warning: when type is in parentheses, array cannot have dynamic size X = new(char*[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:51:31: warning: when type is in parentheses, array cannot have dynamic size I = new(short unsigned int*[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:52:19: warning: when type is in parentheses, array cannot have dynamic size keep = new(char[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:53:22: warning: when type is in parentheses, array cannot have dynamic size display = new(char[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:54:18: warning: when type is in parentheses, array cannot have dynamic size wg = new(float[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:55:19: warning: when type is in parentheses, array cannot have dynamic size nseqs = new(int[maxres+2]); ~ ^~~~~~~~ ~ ./hhalignment.C./hhhmm.C::1442177::2028:: warningwarning: : when type is in parentheses, array cannot have dynamic sizewhen type is in parentheses, array cannot have dynamic size nres=new(int[N_in]); char** lines = new(char*[3*L+100000]); ~ ^~~~ ~ ~ ^~~~~~~~~~ ~ ./hhalignment.C ./hhhmm.C./hhhmm.C:1182:40: warning: when type is in parentheses, array cannot have dynamic size seq[nsa_dssp] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ :150:25: warning: when type is in parentheses, array cannot have dynamic size sname[k]=new(char[strlen(ali.sname[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C./hhalignment.C:156:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(ali.seq[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:162:21: warning: when type is in parentheses, array cannot have dynamic size X[k]=new(char[strlen(ali.seq[k])+2]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:2205:29: warning: when type is in parentheses, array cannot have dynamic size: 167 lines[nline]=new(char[strlen(line)+1]);:35: warning ~ ^~~~~~~~~~~~~~ ~: when type is in parentheses, array cannot have dynamic size I[k]=new(short unsigned int[strlen(ali.seq[k])+2]);./hhhmm.C ~ ^~~~~~~~~~~~~~~~~~~~ ~ :1203:40: warning: when type is in parentheses, array cannot have dynamic size seq[nss_pred] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C:1224:40: warning: when type is in parentheses, array cannot have dynamic size seq[nss_conf] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C:1295:36: warning: when type is in parentheses, array cannot have dynamic size seq[nss_dssp] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhalignment.C:2329:30: warning:: 252when type is in parentheses, array cannot have dynamic size: 31 seq[nss_pred]=new(char[L+2]);: warning: when type is in parentheses, array cannot have dynamic size ~ ^~~ ~ seq[k]=new(char[strlen(cur_seq)+2]); ./hhhmm.C ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:254:29: warning: when type is in parentheses, array cannot have dynamic size X[k]=new(char[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~:2336 : 30./hhalignment.C: warning: when type is in parentheses, array cannot have dynamic size seq[nss_conf]=new(char[L+2]); ~ ^~~ ~ In file included from :256:43: warning: when type is in parentheses, array cannot have dynamic size I[k]=new(short unsigned int[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment.Chhblits.C:143: ./hhalignment.C:47:21: warning: when type is in parentheses, array cannot have dynamic size sname = new(char*[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:48:19: warning: when type is in parentheses, array cannot have dynamic size seq = new(char*[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:49:15: warning: when type is in parentheses, array cannot have dynamic size l = new(int[maxres]); ~ ^~~~~~ ~ ./hhalignment.C:50:17: warning: when type is in parentheses, array cannot have dynamic size X = new(char*[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:51:31: warning: when type is in parentheses, array cannot have dynamic size ./hhhmm.C I = new(short unsigned int*[maxseq+2]);:2177:28: warning: when type is in parentheses, array cannot have dynamic size char** lines = new(char*[3*L+100000]); ~ ^~~~~~~~~~ ~ ~ ^~~~~~~~ ~:315 : 31./hhalignment.C: warning: when type is in parentheses, array cannot have dynamic size sname[k] = new(char[strlen(cur_name)+1]);:52: 19 ~ ^~~~~~~~~~~~~~~~~~ ~: warning: when type is in parentheses, array cannot have dynamic size keep = new(char[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:53:22: warning: when type is in parentheses, array cannot have dynamic size display = new(char[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:54:18: warning: when type is in parentheses, array cannot have dynamic size wg = new(float[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C./hhhmm.C:2177:28: warning: when type is in parentheses, array cannot have dynamic size char** lines = new(char*[3*L+100000]); ~ ^~~~~~~~~~ ~ :55:19: warning: when type is in parentheses, array cannot have dynamic size nseqs = new(int[maxres+2]); ~ ^~~~~~~~ ~ ./hhhmm.C:2205:29: warning: when type is in parentheses, array cannot have dynamic size lines[nline]=new(char[strlen(line)+1]); ~ ^~~~~~~~~~~~~~ ~ ./hhalignment.C./hhhmm.C:144:20: warning: when type is in parentheses, array cannot have dynamic size nres=new(int[N_in]); ~ ^~~~ ~ ./hhalignment.C:150:25: warning: when type is in parentheses, array cannot have dynamic size sname[k]=new(char[strlen(ali.sname[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:156:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(ali.seq[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:162:21: warning: when type is in parentheses, array cannot have dynamic size X[k]=new(char[strlen(ali.seq[k])+2]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:468:29: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(cur_seq)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:2205:29: warning: when type is in parentheses, array cannot have dynamic size lines[nline]=new(char[strlen(line)+1]); ~ ^~~~~~~~~~~~~~ ~ :167:35: warning: when type is in parentheses, array cannot have dynamic size I[k]=new(short unsigned int[strlen(ali.seq[k])+2]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:2329:30: warning: when type is in parentheses, array cannot have dynamic size seq[nss_pred]=new(char[L+2]); ~ ^~~ ~ ./hhhmm.C:2336:30: warning: when type is in parentheses, array cannot have dynamic size seq[nss_conf]=new(char[L+2]); ~ ^~~ ~ In file included from hhalign.C:96: ./hhalignment.C:47:21: warning: when type is in parentheses, array cannot have dynamic size sname = new(char*[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:48:19: warning: when type is in parentheses, array cannot have dynamic size seq = new(char*[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:49:15: warning: when type is in parentheses, array cannot have dynamic size l = new(int[maxres]); ~ ^~~~~~ ~ ./hhalignment.C:50:17: warning: when type is in parentheses, array cannot have dynamic size X = new(char*[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:51:31: warning: when type is in parentheses, array cannot have dynamic size I = new(short unsigned int*[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:52:19: warning: when type is in parentheses, array cannot have dynamic size keep = new(char[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:53:22: warning: when type is in parentheses, array cannot have dynamic size display = new(char[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:54:18: warning: when type is in parentheses, array cannot have dynamic size wg = new(float[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:55:19: warning: when type is in parentheses, array cannot have dynamic size nseqs = new(int[maxres+2]); ~ ^~~~~~~~ ~ ./hhhmm.C:1471:27: warning: when type is in parentheses, array cannot have dynamic size sname[k+1]=new(char[strlen(longname)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:1473:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[L+2]); ~ ^~~ ~ ./hhhmm.C:1476:25: warning: when type is in parentheses, array cannot have dynamic size seq[k+1]=new(char[L+2]); ~ ^~~ ~ ./hhhmm.C:1494:25: warning: when type is in parentheses, array cannot have dynamic size sname[k]=new(char[strlen(longname)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:1496:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C./hhhmm.C:2329:30: warning: when type is in parentheses, array cannot have dynamic size seq[nss_pred]=new(char[L+2]); ~ ^~~ ~ ./hhhmm.C:2336:30: warning: when type is in parentheses, array cannot have dynamic size seq[nss_conf]=new(char[L+2]); ~ ^~~ ~ In file included from hhfilter.C:82: ./hhalignment.C:47:21: warning: when type is in parentheses, array cannot have dynamic size sname = new(char*[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:48:19: warning: when type is in parentheses, array cannot have dynamic size seq = new(char*[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:49:15: warning: when type is in parentheses, array cannot have dynamic size l = new(int[maxres]); ~ ^~~~~~ ~ ./hhalignment.C:50:17: warning: when type is in parentheses, array cannot have dynamic size X = new(char*[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:144:20: warning: when type is in parentheses, array cannot have dynamic size nres=new(int[N_in]); ~ ^~~~ ~ ./hhalignment.C:150:25: warning: when type is in parentheses, array cannot have dynamic size sname[k]=new(char[strlen(ali.sname[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:156:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(ali.seq[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ :252:31./hhalignment.C:162:21: warning: when type is in parentheses, array cannot have dynamic size X[k]=new(char[strlen(ali.seq[k])+2]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ : warning: when type is in parentheses, array cannot have dynamic size ./hhalignment.C:167:35: warning: when type is in parentheses, array cannot have dynamic size I[k]=new(short unsigned int[strlen(ali.seq[k])+2]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ seq[k]=new(char[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:254:29: warning: when type is in parentheses, array cannot have dynamic size X[k]=new(char[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:256:43: warning: when type is in parentheses, array cannot have dynamic size I[k]=new(short unsigned int[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:51:31: warning: when type is in parentheses, array cannot have dynamic size I = new(short unsigned int*[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:52:19: warning: when type is in parentheses, array cannot have dynamic size keep = new(char[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:53:22: warning: when type is in parentheses, array cannot have dynamic size display = new(char[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:54:18: warning: when type is in parentheses, array cannot have dynamic size wg = new(float[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:55:19: warning: when type is in parentheses, array cannot have dynamic size nseqs = new(int[maxres+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:144:20: warning: when type is in parentheses, array cannot have dynamic size nres=new(int[N_in]); ~ ^~~~ ~ ./hhalignment.C:150:25: warning: when type is in parentheses, array cannot have dynamic size sname[k]=new(char[strlen(ali.sname[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:156:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(ali.seq[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:162:21: warning: when type is in parentheses, array cannot have dynamic size X[k]=new(char[strlen(ali.seq[k])+2]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:167:35: warning: when type is in parentheses, array cannot have dynamic size I[k]=new(short unsigned int[strlen(ali.seq[k])+2]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:252:31: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:254:29: warning: when type is in parentheses, array cannot have dynamic size X[k]=new(char[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:256:43: warning: when type is in parentheses, array cannot have dynamic size I[k]=new(short unsigned int[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:315:31: warning: when type is in parentheses, array cannot have dynamic size sname[k] = new(char[strlen(cur_name)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:252:31: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:254:29: warning: when type is in parentheses, array cannot have dynamic size X[k]=new(char[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:256:43: warning: when type is in parentheses, array cannot have dynamic size I[k]=new(short unsigned int[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:315:31: warning: when type is in parentheses, array cannot have dynamic size sname[k] = new(char[strlen(cur_name)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:315:31: warning: when type is in parentheses, array cannot have dynamic size sname[k] = new(char[strlen(cur_name)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C./hhalignment.C:431:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:433:21: warning: when type is in parentheses, array cannot have dynamic size X[k]=new(char[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:435:35: warning: when type is in parentheses, array cannot have dynamic size I[k]=new(short unsigned int[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ :719:40: warning: when type is in parentheses, array cannot have dynamic size seq[nsa_dssp] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C./hhalignment.C:740:40: warning: when type is in parentheses, array cannot have dynamic size seq[nss_pred] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C:./hhalignment.C761:40: warning: when type is in parentheses, array cannot have dynamic size seq[nss_conf] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C:431:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:835:36: warning: when type is in parentheses, array cannot have dynamic size seq[nss_dssp] = new(char[par.maxres+2]);:433: 21 ~ ^~~~~~~~~~~~ ~ : warning./hhalignment.C:431:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ : when type is in parentheses, array cannot have dynamic size ./hhalignment.C:433:21: warning: when type is in parentheses, array cannot have dynamic size X[k]=new(char[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ X[k]=new(char[strlen(cur_seq)+2]); ./hhalignment.C:435:35: warning: when type is in parentheses, array cannot have dynamic size I[k]=new(short unsigned int[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:649:31: warning: when type is in parentheses, array cannot have dynamic size if (nres==NULL) nres=new(int[N_in]); ~ ^~~~ ~: 435 : 35./hhhmm.C:2177:28: warning: when type is in parentheses, array cannot have dynamic size char** lines = new(char*[3*L+100000]); ~ ^~~~~~~~~~ ~ : warning: when type is in parentheses, array cannot have dynamic size I[k]=new(short unsigned int[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:2205:29: warning: when type is in parentheses, array cannot have dynamic size lines[nline]=new(char[strlen(line)+1]); ~ ^~~~~~~~~~~~~~ ~ ./hhhmm.C:2329:30: warning: when type is in parentheses, array cannot have dynamic size seq[nss_pred]=new(char[L+2]); ~ ^~~ ~ ./hhhmm.C./hhalignment.C:431:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:433:21: warning: when type is in parentheses, array cannot have dynamic size X[k]=new(char[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:435:35: warning: when type is in parentheses, array cannot have dynamic size I[k]=new(short unsigned int[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ :2336:30: warning: when type is in parentheses, array cannot have dynamic size seq[nss_conf]=new(char[L+2]); ~ ^~~ ~ In file included from hhsearch.C:113: ./hhalignment.C:47:21: warning: when type is in parentheses, array cannot have dynamic size sname = new(char*[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:48:19: warning: when type is in parentheses, array cannot have dynamic size seq = new(char*[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:49:15: warning: when type is in parentheses, array cannot have dynamic size l = new(int[maxres]); ~ ^~~~~~ ~ ./hhalignment.C:50:17: warning: when type is in parentheses, array cannot have dynamic size X = new(char*[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:51:31: warning: when type is in parentheses, array cannot have dynamic size I = new(short unsigned int*[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:52:19: warning: when type is in parentheses, array cannot have dynamic size keep = new(char[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:53:22: warning: when type is in parentheses, array cannot have dynamic size display = new(char[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:54:18: warning: when type is in parentheses, array cannot have dynamic size wg = new(float[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:55:19: warning: when type is in parentheses, array cannot have dynamic size nseqs = new(int[maxres+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:144:20: warning: when type is in parentheses, array cannot have dynamic size nres=new(int[N_in]); ~ ^~~~ ~ ./hhalignment.C:150:25: warning: when type is in parentheses, array cannot have dynamic size sname[k]=new(char[strlen(ali.sname[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:156:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(ali.seq[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C./hhalignment.C./hhalignment.C:649:31: warning: when type is in parentheses, array cannot have dynamic size if (nres==NULL) nres=new(int[N_in]); ~ ^~~~ ~ :162:21: warning: when type is in parentheses, array cannot have dynamic size X[k]=new(char[strlen(ali.seq[k])+2]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ :649:31: warning./hhalignment.C:167:35: warning: when type is in parentheses, array cannot have dynamic size I[k]=new(short unsigned int[strlen(ali.seq[k])+2]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ : when type is in parentheses, array cannot have dynamic size if (nres==NULL) nres=new(int[N_in]); ~ ^~~~ ~ ./hhhmm.C./hhalignment.C:649:31: warning: when type is in parentheses, array cannot have dynamic size if (nres==NULL) nres=new(int[N_in]); ~ ^~~~ ~ ./hhalignment.C:1009:27: warning: when type is in parentheses, array cannot have dynamic size sname[k+1]=new(char[strlen(longname)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:252:31: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment.C :254:29: warning: when type is in parentheses, array cannot have dynamic size X[k]=new(char[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:256:43: warning: when type is in parentheses, array cannot have dynamic size I[k]=new(short unsigned int[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:1011:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[L+2]); ~ ^~~ ~ ./hhhmm.C:1014:25: warning: when type is in parentheses, array cannot have dynamic size seq[k+1]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:315:31: warning: when type is in parentheses, array cannot have dynamic size sname[k] = new(char[strlen(cur_name)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:1032:25: warning: when type is in parentheses, array cannot have dynamic size sname[k]=new(char[strlen(longname)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:1034:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[L+2]); ~ ^~~ ~ :923:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(q->seq[qk])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:926:21: warning: when type is in parentheses, array cannot have dynamic size X[k]=new(char[strlen(q->seq[qk])+1]);./hhhmm.C ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:928:35: warning: when type is in parentheses, array cannot have dynamic size I[k]=new(short unsigned int[strlen(q->seq[qk])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:949:27: warning: when type is in parentheses, array cannot have dynamic size sname[k] = new(char[strlen(q->sname[qk])+1]); ~ ^~~~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:972:26: warning: when type is in parentheses, array cannot have dynamic size char *dummy = new(char[N_in+1]); ~ ^~~~~~ ~ ./hhalignment.C:1182:40: warning: when type is in parentheses, array cannot have dynamic size seq[nsa_dssp] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~ ./hhhmm.C:1203:40: :warning1031: :when type is in parentheses, array cannot have dynamic size21 : seq[nss_pred] = new(char[par.maxres+2]); warning: when type is in parentheses, array cannot have dynamic size ~ ^~~~~~~~~~~~ ~ char* in=new(char[N_in+1]); // in[k]=1: seq k has been accepted; in[k]=0: seq k has not yet been accepted at current seqid ./hhhmm.C ~ ^~~~~~ ~ ./hhalignment.C:1032:23: warning: when type is in parentheses, array cannot have dynamic size char* inkk=new(char[N_in+1]); // inkk[k]=1 iff in[ksort[k]]=1 else 0; ~ ^~~~~~ ~ ./hhalignment.C:1033:21: warning: when type is in parentheses, array cannot have dynamic size int* Nmax=new(int[L+2]); // position-dependent maximum-sequence-identity threshold for filtering? (variable used in former version was idmax):1224 : ~ ^~~ ~40 : ./hhalignment.Cwarning: when type is in parentheses, array cannot have dynamic size seq[nss_conf] = new(char[par.maxres+2]); ~ ^~~~~~~~~~~~ ~: 1034 : 25./hhalignment.C:923:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(q->seq[qk])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ : warning: when type is in parentheses, array cannot have dynamic size ./hhalignment.C:926:21: warning: when type is in parentheses, array cannot have dynamic size X[k]=new(char[strlen(q->seq[qk])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ int* idmaxwin=new(int[L+2]); // minimum value of idmax[i-WFIL,i+WFIL] ./hhalignment.C:928:35: warning: when type is in parentheses, array cannot have dynamic size I[k]=new(short unsigned int[strlen(q->seq[qk])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ~ ^~~ ~ ./hhalignment.C:1035:27: warning: when type is in parentheses, array cannot have dynamic size int* seqid_prev=new(int[N_in+1]); // maximum-sequence-identity threshold used in previous round of filtering (with lower seqid) ./hhalignment.C:949:27: warning: when type is in parentheses, array cannot have dynamic size sname[k] = new(char[strlen(q->sname[qk])+1]); ~ ^~~~~~~~~~~~~~~~~~~~~~ ~ ~ ^~~~~~ ~ ./hhalignment.C:1036./hhalignment.C::972:26: warning: when type is in parentheses, array cannot have dynamic size char *dummy = new(char[N_in+1]); ~ ^~~~~~ ~ 18: warning: when type is in parentheses, array cannot have dynamic size int* N=new(int[L+2]); // N[i] number of already accepted sequences at position i ~ ^~~ ~ ./hhalignment.C./hhhmm.C:1064:21: warning: when type is in parentheses, array cannot have dynamic size first=new(int[N_in]);// first non-gap position in sequence k ~ ^~~~ ~ ./hhalignment.C:1065:21: warning: when type is in parentheses, array cannot have dynamic size last =new(int[N_in]);// last non-gap position in sequence k ~ ^~~~ ~ ./hhalignment.C:1079:20: warning: when type is in parentheses, array cannot have dynamic size nres=new(int[N_in]); ~ ^~~~ ~ ./hhalignment.C:1295:36: warning: when type is in parentheses, array cannot have dynamic size seq[nss_dssp] = new(char[par.maxres+2]);:1095:21: warning : ~ ^~~~~~~~~~~~ ~ when type is in parentheses, array cannot have dynamic size ksort=new(int[N_in]); // never reuse alignment object for new alignment with more sequences./hhalignment.C:1031:21: warning: when type is in parentheses, array cannot have dynamic size char* in=new(char[N_in+1]); // in[k]=1: seq k has been accepted; in[k]=0: seq k has not yet been accepted at current seqid ~ ^~~~~~ ~ ./hhalignment.C:1032:23: warning: when type is in parentheses, array cannot have dynamic size char* inkk=new(char[N_in+1]); // inkk[k]=1 iff in[ksort[k]]=1 else 0; ~ ^~~~~~ ~ ./hhalignment.C:1033:21: warning: when type is in parentheses, array cannot have dynamic size int* Nmax=new(int[L+2]); // position-dependent maximum-sequence-identity threshold for filtering? (variable used in former version was idmax) ~ ^~~ ~ ./hhalignment.C:1034:25: warning: when type is in parentheses, array cannot have dynamic size int* idmaxwin=new(int[L+2]); // minimum value of idmax[i-WFIL,i+WFIL] ~ ^~~ ~ ./hhalignment.C:1035:27: warning: when type is in parentheses, array cannot have dynamic size int* seqid_prev=new(int[N_in+1]); // maximum-sequence-identity threshold used in previous round of filtering (with lower seqid) ~ ^~~~~~ ~ ./hhalignment.C:1036:18: warning: when type is in parentheses, array cannot have dynamic size int* N=new(int[L+2]); // N[i] number of already accepted sequences at position i ~ ^~~ ~ ./hhalignment.C:1064:21: warning: when type is in parentheses, array cannot have dynamic size first=new(int[N_in]);// first non-gap position in sequence k ~ ^~~~ ~ ./hhalignment.C:1065:21: warning: when type is in parentheses, array cannot have dynamic size last =new(int[N_in]);// last non-gap position in sequence k ~ ^~~~ ~ ~ ^~~~ ~ ./hhalignment.C:1079:20: warning: when type is in parentheses, array cannot have dynamic size nres=new(int[N_in]); ~ ^~~~ ~ ./hhalignment.C:1095:21: warning: when type is in parentheses, array cannot have dynamic size ksort=new(int[N_in]); // never reuse alignment object for new alignment with more sequences ~ ^~~~ ~ ./hhalignment.C./hhalignment.C:923:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(q->seq[qk])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ :923:23: ./hhalignment.C:926:21: warning: when type is in parentheses, array cannot have dynamic size X[k]=new(char[strlen(q->seq[qk])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ warning: ./hhalignment.Cwhen type is in parentheses, array cannot have dynamic size:928:35: warning: when type is in parentheses, array cannot have dynamic size I[k]=new(short unsigned int[strlen(q->seq[qk])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ seq[k]=new(char[strlen(q->seq[qk])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:./hhalignment.C:949:27: warning: when type is in parentheses, array cannot have dynamic size sname[k] = new(char[strlen(q->sname[qk])+1]); ~ ^~~~~~~~~~~~~~~~~~~~~~ ~ 926:21: warning: when type is in parentheses, array cannot have dynamic size X[k]=new(char[strlen(q->seq[qk])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:972:26: warning: when type is in parentheses, array cannot have dynamic size char *dummy = new(char[N_in+1]); ~ ^~~~~~ ~ ./hhalignment.C:928:35: warning: when type is in parentheses, array cannot have dynamic size I[k]=new(short unsigned int[strlen(q->seq[qk])+1]); ./hhalignment.C:1031:21: warning: when type is in parentheses, array cannot have dynamic size char* in=new(char[N_in+1]); // in[k]=1: seq k has been accepted; in[k]=0: seq k has not yet been accepted at current seqid ~ ^~~~~~ ~ ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C./hhalignment.C:1303:30: warning: when type is in parentheses, array cannot have dynamic size float** logodds=new(float*[L+1]); // log-odds ratios for HMM qcore ~ ^~~ ~ ./hhalignment.C:1312:21: warning: when type is in parentheses, array cannot have dynamic size first=new(int[N_in]);// first non-gap position in sequence k ~ ^~~~ ~ ./hhalignment.C:1313:21: warning: when type is in parentheses, array cannot have dynamic size last =new(int[N_in]);// last non-gap position in sequence k ~ ^~~~ ~ ./hhalignment.C::9491303::2730:: warningwarning: : when type is in parentheses, array cannot have dynamic sizewhen type is in parentheses, array cannot have dynamic size sname[k] = new(char[strlen(q->sname[qk])+1]); float** logodds=new(float*[L+1]); // log-odds ratios for HMM qcore ~ ^~~~~~~~~~~~~~~~~~~~~~ ~ ~ ^~~ ~ ./hhalignment.C./hhalignment.C:1312:21: warning: when type is in parentheses, array cannot have dynamic size ./hhalignment.C:431:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ first=new(int[N_in]);// first non-gap position in sequence k./hhalignment.C :433:21: warning: when type is in parentheses, array cannot have dynamic size X[k]=new(char[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ~ ^~~~ ~ ./hhalignment.C:435:35: warning: when type is in parentheses, array cannot have dynamic size I[k]=new(short unsigned int[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:972:26::1313 :warning21: :when type is in parentheses, array cannot have dynamic size warning char *dummy = new(char[N_in+1]);: when type is in parentheses, array cannot have dynamic size last =new(int[N_in]);// last non-gap position in sequence k ~ ^~~~~~ ~ ./hhalignment.C:1032:23: warning: when type is in parentheses, array cannot have dynamic size char* inkk=new(char[N_in+1]); // inkk[k]=1 iff in[ksort[k]]=1 else 0; ~ ^~~~~~ ~ ./hhalignment.C:1033:21: warning: when type is in parentheses, array cannot have dynamic size int* Nmax=new(int[L+2]); // position-dependent maximum-sequence-identity threshold for filtering? (variable used in former version was idmax) ~ ^~~ ~ ./hhalignment.C:1034:25: warning: when type is in parentheses, array cannot have dynamic size int* idmaxwin=new(int[L+2]); // minimum value of idmax[i-WFIL,i+WFIL] ~ ^~~~ ~ ~ ^~~ ~ ./hhalignment.C:1035:27: warning: when type is in parentheses, array cannot have dynamic size int* seqid_prev=new(int[N_in+1]); // maximum-sequence-identity threshold used in previous round of filtering (with lower seqid) ~ ^~~~~~ ~ ./hhalignment.C:1036:18: warning: when type is in parentheses, array cannot have dynamic size int* N=new(int[L+2]); // N[i] number of already accepted sequences at position i ~ ^~~ ~ ./hhalignment.C:1064:21: warning: when type is in parentheses, array cannot have dynamic size first=new(int[N_in]);// first non-gap position in sequence k ~ ^~~~ ~ ./hhalignment.C:1065:21: warning: when type is in parentheses, array cannot have dynamic size last =new(int[N_in]);// last non-gap position in sequence k ~ ^~~~ ~ ./hhalignment.C:1079:20: warning: when type is in parentheses, array cannot have dynamic size nres=new(int[N_in]); ~ ^~~~ ~ ./hhalignment.C:1326:20./hhalignment.C::1095:21: warning: when type is in parentheses, array cannot have dynamic size ksort=new(int[N_in]); // never reuse alignment object for new alignment with more sequences ~ ^~~~ ~ warning: when type is in parentheses, array cannot have dynamic size nres=new(int[N_in]);./hhalignment.C ~ ^~~~ ~ ./hhalignment.C:1326:20: warning: when type is in parentheses, array cannot have dynamic size nres=new(int[N_in]); ~ ^~~~ ~ :1031:21: warning: when type is in parentheses, array cannot have dynamic size char* in=new(char[N_in+1]); // in[k]=1: seq k has been accepted; in[k]=0: seq k has not yet been accepted at current seqid ~ ^~~~~~ ~ ./hhalignment.C:1032:23: warning: when type is in parentheses, array cannot have dynamic size char* inkk=new(char[N_in+1]); // inkk[k]=1 iff in[ksort[k]]=1 else 0; ./hhalignment.C:1303:30: warning: when type is in parentheses, array cannot have dynamic size float** logodds=new(float*[L+1]); // log-odds ratios for HMM qcore ~ ^~~ ~ ~ ^~~~~~ ~ ./hhalignment.C:1312:21: warning: when type is in parentheses, array cannot have dynamic size first=new(int[N_in]);// first non-gap position in sequence k ~ ^~~~ ~ ./hhalignment.C:1313:21: warning: when type is in parentheses, array cannot have dynamic size last =new(int[N_in]);// last non-gap position in sequence k ~ ^~~~ ~ ./hhalignment.C:1033:21:./hhalignment.C: 1326:20: warning: when type is in parentheses, array cannot have dynamic size nres=new(int[N_in]); ~ ^~~~ ~ warning: when type is in parentheses, array cannot have dynamic size int* Nmax=new(int[L+2]); // position-dependent maximum-sequence-identity threshold for filtering? (variable used in former version was idmax) ~ ^~~ ~ ./hhalignment.C:1034:25: warning: when type is in parentheses, array cannot have dynamic size int* idmaxwin=new(int[L+2]); // minimum value of idmax[i-WFIL,i+WFIL] ~ ^~~ ~ ./hhalignment.C:1035:27: warning: when type is in parentheses, array cannot have dynamic size int* seqid_prev=new(int[N_in+1]); // maximum-sequence-identity threshold used in previous round of filtering (with lower seqid) ~ ^~~~~~ ~ ./hhalignment.C:1036:18: warning: when type is in parentheses, array cannot have dynamic size int* N=new(int[L+2]); // N[i] number of already accepted sequences at position i ~ ^~~ ~ ./hhalignment.C:1064:21: warning: when type is in parentheses, array cannot have dynamic size first=new(int[N_in]);// first non-gap position in sequence k ~ ^~~~ ~ ./hhalignment.C:1065:21: warning: when type is in parentheses, array cannot have dynamic size last =new(int[N_in]);// last non-gap position in sequence k ~ ^~~~ ~ ./hhalignment.C:1079:20: warning: when type is in parentheses, array cannot have dynamic size nres=new(int[N_in]); ~ ^~~~ ~ ./hhalignment.C:1095:21: warning: when type is in parentheses, array cannot have dynamic size ksort=new(int[N_in]); // never reuse alignment object for new alignment with more sequences ~ ^~~~ ~ ./hhalignment.C:1598:37: warning: when type is in parentheses, array cannot have dynamic size q->seq[q->ncons]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:1605:40: warning: when type is in parentheses, array cannot have dynamic size q->sname[q->nfirst]=new(char[strlen(name)+11]); ~ ^~~~~~~~~~~~~~~ ~ ./hhalignment.C:1609:38: warning: when type is in parentheses, array cannot have dynamic size q->seq[q->nfirst]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C./hhalignment.C./hhhmm.C:1598:37: warning: when type is in parentheses, array cannot have dynamic size q->seq[q->ncons]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:1605:40: warning: when type is in parentheses, array cannot have dynamic size q->sname[q->nfirst]=new(char[strlen(name)+11]); ~ ^~~~~~~~~~~~~~~ ~ ./hhalignment.C:1303:30: warning: when type is in parentheses, array cannot have dynamic size float** logodds=new(float*[L+1]); // log-odds ratios for HMM qcore ~ ^~~ ~ ./hhalignment.C:1661:33: warning: when type is in parentheses, array cannot have dynamic size q->sname[nn]=new(char[strlen(sname[k])+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ::14711609::2738./hhalignment.C:1664:31: warning: when type is in parentheses, array cannot have dynamic size q->seq[nn]=new(char[strlen(seq[k])+1]); ~ ^~~~~~~~~~~~~~~~ ~ :: warningwarning: : when type is in parentheses, array cannot have dynamic sizewhen type is in parentheses, array cannot have dynamic size sname[k+1]=new(char[strlen(longname)+1]); q->seq[q->nfirst]=new(char[L+2]); ~ ^~~ ~./hhalignment.C ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C./hhalignment.C./hhhmm.C:649:31: warning: when type is in parentheses, array cannot have dynamic size if (nres==NULL) nres=new(int[N_in]); ~ ^~~~ ~ :1312:21: warning: when type is in parentheses, array cannot have dynamic size first=new(int[N_in]);// first non-gap position in sequence k:1473: 23 ~ ^~~~ ~ : warning./hhalignment.C: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[L+2]); ~ ^~~ ~: 1313 :./hhhmm.C21: warning: when type is in parentheses, array cannot have dynamic size last =new(int[N_in]);// last non-gap position in sequence k ~ ^~~~ ~: 1476 : 25./hhalignment.C: warning: when type is in parentheses, array cannot have dynamic size seq[k+1]=new(char[L+2]); ~ ^~~ ~ ./hhhmm.C:1326:20: warning: when type is in parentheses, array cannot have dynamic size nres=new(int[N_in]); ~ ^~~~ ~ ./hhalignment.C:1598:37: warning: when type is in parentheses, array cannot have dynamic size q->seq[q->ncons]=new(char[L+2]); ~ ^~~ ~ :1494./hhalignment.C:1605:40: warning: when type is in parentheses, array cannot have dynamic size q->sname[q->nfirst]=new(char[strlen(name)+11]); ~ ^~~~~~~~~~~~~~~ ~ :25: warning: when type is in parentheses, array cannot have dynamic size ./hhalignment.C:1609:38: warning: when type is in parentheses, array cannot have dynamic size q->seq[q->nfirst]=new(char[L+2]); ~ ^~~ ~ sname[k]=new(char[strlen(longname)+1]);./hhalignment.C:1661:33: warning: when type is in parentheses, array cannot have dynamic size q->sname[nn]=new(char[strlen(sname[k])+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhhmm.C:1496:23: warning: when type is in parentheses, array cannot have dynamic size ./hhalignment.C:1764:16: warning: when type is in parentheses, array cannot have dynamic size n = new(int*[L+2]); ~ ^~~ ~ seq[k]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:1826:57: warning: add explicit braces to avoid dangling else [-Wdangling-else] if(in[k] && X[k][i]sname[nn]=new(char[strlen(sname[k])+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:1664:31: warning: when type is in parentheses, array cannot have dynamic size q->seq[nn]=new(char[strlen(seq[k])+1]); ~ ^~~~~~~~~~~~~~~~ ~ ./hhalignment.C./hhalignment.C:1664:31: warning: when type is in parentheses, array cannot have dynamic size q->seq[nn]=new(char[strlen(seq[k])+1]); ~ ^~~~~~~~~~~~~~~~ ~ ./hhalignment.C:1764:16: warning: when type is in parentheses, array cannot have dynamic size n = new(int*[L+2]); ~ ^~~ ~ ./hhalignment.C:1980:16: warning: when type is in parentheses, array cannot have dynamic size n = new(int*[L+2]); ~ ^~~ ~ :1764:16: warning: when type is in parentheses, array cannot have dynamic size n = new(int*[L+2]);./hhalignment.C:2047:55: warning: add explicit braces to avoid dangling else [-Wdangling-else] if(in[k] && I[k][i]>0) wi[k]=wg[k]; else wi[k]=0.0; ^ ~ ^~~ ~ ./hhalignment.C./hhalignment.C./hhalignment.C:1826:57: warning: add explicit braces to avoid dangling else [-Wdangling-else] if(in[k] && X[k][i]seq[q->ncons]=new(char[L+2]);:57: warning : ~ ^~~ ~ add explicit braces to avoid dangling else [-Wdangling-else] if(in[k] && X[k][i]sname[q->nfirst]=new(char[strlen(name)+11]); ~ ^~~~~~~~~~~~~~~ ~ ./hhalignment.C:1609:38: warning: when type is in parentheses, array cannot have dynamic size q->seq[q->nfirst]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:2243:58: warning: add explicit braces to avoid dangling else [-Wdangling-else] if(in[k] && X[k][i]==GAP) wi[k]=wg[k]; else wi[k]=0.0; ^ ./hhalignment.C./hhalignment.C:1980:16: warning: when type is in parentheses, array cannot have dynamic size n = new(int*[L+2]); ~ ^~~ ~ ./hhalignment.C:1661:33: warning: when type is in parentheses, array cannot have dynamic size q->sname[nn]=new(char[strlen(sname[k])+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:2047:55: warning: add explicit braces to avoid dangling else [-Wdangling-else] if(in[k] && I[k][i]>0) wi[k]=wg[k]; else wi[k]=0.0; ^ :1980:16: warning: when type is in parentheses, array cannot have dynamic size n = new(int*[L+2]); ~ ^~~ ~ ./hhalignment.C ./hhalignment.C:1664:31: warning: when type is in parentheses, array cannot have dynamic size q->seq[nn]=new(char[strlen(seq[k])+1]); ~ ^~~~~~~~~~~~~~~~ ~ ./hhalignment.C:2047:55: warning: add explicit braces to avoid dangling else [-Wdangling-else] if(in[k] && I[k][i]>0) wi[k]=wg[k]; else wi[k]=0.0; ^ ./hhalignment.C./hhalignment.C:923:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(q->seq[qk])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:926:21: warning: when type is in parentheses, array cannot have dynamic size X[k]=new(char[strlen(q->seq[qk])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:928:35: warning: when type is in parentheses, array cannot have dynamic size I[k]=new(short unsigned int[strlen(q->seq[qk])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:949:27: warning: when type is in parentheses, array cannot have dynamic size sname[k] = new(char[strlen(q->sname[qk])+1]); ~ ^~~~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:2173:16: warning: when type is in parentheses, array cannot have dynamic size n = new(int*[L+2]); ~ ^~~ ~ ./hhalignment.C:2243:58: warning: add explicit braces to avoid dangling else [-Wdangling-else] if(in[k] && X[k][i]==GAP) wi[k]=wg[k]; else wi[k]=0.0; ^ :1764:16: warning: when type is in parentheses, array cannot have dynamic size n = new(int*[L+2]); ~ ^~~ ~ ./hhalignment.C:2173:16: warning: when type is in parentheses, array cannot have dynamic size n = new(int*[L+2]); ~ ^~~ ~ ./hhalignment.C./hhalignment.C:2430:28: warning: when type is in parentheses, array cannot have dynamic size char* cur_seq = new(char[par.maxcol]); // Sequence currently read in ~ ^~~~~~~~~~ ~ ./hhalignment.C:2442:23: warning: when type is in parentheses, array cannot have dynamic size int* imatch=new(int[hit.j2+1]); ~ ^~~~~~~~ ~ ./hhalignment.C:972:26: warning: when type is in parentheses, array cannot have dynamic size char *dummy = new(char[N_in+1]); ~ ^~~~~~ ~ :1826:57: warning: add explicit braces to avoid dangling else [-Wdangling-else] if(in[k] && X[k][i]0) wi[k]=wg[k]; else wi[k]=0.0; ^ ./hhalignment.C:2743:20: warning: when type is in parentheses, array cannot have dynamic size n = new(int*[L+2]); ~ ^~~ ~ ./hhalignment.C:1312:21: warning: when type is in parentheses, array cannot have dynamic size first=new(int[N_in]);// first non-gap position in sequence k ~ ^~~~ ~ ./hhalignment.C:1313:21: warning: when type is in parentheses, array cannot have dynamic size last =new(int[N_in]);// last non-gap position in sequence k ~ ^~~~ ~ ./hhalignment.C:1326:20: warning: when type is in parentheses, array cannot have dynamic size nres=new(int[N_in]); ~ ^~~~ ~ ./hhalignment.C./hhalignment.C:2587:26: warning: when type is in parentheses, array cannot have dynamic size seq[N_in]=new(char[h]); ~ ^ ~ ./hhalignment.C:2590:24: warning: when type is in parentheses, array cannot have dynamic size X[N_in]=new(char[h]); ~ ^ ~ ./hhalignment.C:2592:38: warning: when type is in parentheses, array cannot have dynamic size I[N_in]=new(short unsigned int[h]); ~ ^ ~ ./hhalignment.C:2594:28: warning: when type is in parentheses, array cannot have dynamic size sname[N_in]=new(char[strlen(Tali.sname[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:2625:20: warning: when type is in parentheses, array cannot have dynamic size X[N_in]=new(char[L+2]); ~ ^~~ ~ :2173:16: warning: when type is in parentheses, array cannot have dynamic size./hhalignment.C:2663:26: warning: when type is in parentheses, array cannot have dynamic size seq[N_in]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:2665:24: warning: when type is in parentheses, array cannot have dynamic size X[N_in]=new(char[L+2]); ~ ^~~ ~ n = new(int*[L+2]);./hhalignment.C:2667:38: warning: when type is in parentheses, array cannot have dynamic size I[N_in]=new(short unsigned int[L+2]); ~ ^~~ ~ ./hhalignment.C ~ ^~~ ~ : 2430./hhalignment.C:2686:26: warning: when type is in parentheses, array cannot have dynamic size seq[N_in]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C::2688:24: warning: when type is in parentheses, array cannot have dynamic size X[N_in]=new(char[L+2]); ~ ^~~ ~ 28: warning: when type is in parentheses, array cannot have dynamic size char* cur_seq = new(char[par.maxcol]); // Sequence currently read inIn file included from hhalign.C:97: ./hhhit.C:141:17: warning: when type is in parentheses, array cannot have dynamic size bMM=new(char*[Nq]); ~ ^~ ~ ./hhhit.C:142:17: warning: when type is in parentheses, array cannot have dynamic size bMI=new(char*[Nq]); ~ ^~ ~ ./hhhit.C:143:17: warning: when type is in parentheses, array cannot have dynamic size bIM=new(char*[Nq]); ~ ^~ ~ ./hhhit.C:144:17: warning: when type is in parentheses, array cannot have dynamic size bDG=new(char*[Nq]); ~ ^~ ~ ./hhhit.C:145:17: warning: when type is in parentheses, array cannot have dynamic size bGD=new(char*[Nq]); ~ ^~ ~ ./hhhit.C:146:22: warning: when type is in parentheses, array cannot have dynamic size cell_off=new(char*[Nq]); ~ ^~ ~ ./hhhit.C:149:23: warning: when type is in parentheses, array cannot have dynamic size bMM[i]=new(char[Nt]); ~ ^~ ~ ./hhhit.C:150:23: warning: when type is in parentheses, array cannot have dynamic size bMI[i]=new(char[Nt]); ~ ^~ ~ ./hhhit.C:151:23: warning: when type is in parentheses, array cannot have dynamic size bIM[i]=new(char[Nt]); ~ ^~ ~ ./hhhit.C:152:23: warning: when type is in parentheses, array cannot have dynamic size bGD[i]=new(char[Nt]); ~ ^~ ~ ./hhhit.C:153:23: warning: when type is in parentheses, array cannot have dynamic size bDG[i]=new(char[Nt]); ~ ^~ ~ ./hhhit.C:154:28: warning: when type is in parentheses, array cannot have dynamic size cell_off[i]=new(char[Nt]); ~ ^~ ~ ~ ^~~~~~~~~~ ~ ./hhalignment.C./hhhit.C:192:20: warning: when type is in parentheses, array cannot have dynamic size F_MM=new(double*[Nq]); ~ ^~ ~ ./hhhit.C:199:20: warning: when type is in parentheses, array cannot have dynamic size scale=new(double[Nq+1]); // need Nq+3? ~ ^~~~ ~ :./hhhit.C2442:202:28: warning: when type is in parentheses, array cannot have dynamic size F_MM[i] = new(double[Nt]); ~ ^~ ~ ./hhalignment.C:1598:37: warning: when type is in parentheses, array cannot have dynamic size q->seq[q->ncons]=new(char[L+2]); ~ ^~~ ~ :23: warning./hhalignment.C: :1605:40: warning: when type is in parentheses, array cannot have dynamic size q->sname[q->nfirst]=new(char[strlen(name)+11]); ~ ^~~~~~~~~~~~~~~ ~ when type is in parentheses, array cannot have dynamic size int* imatch=new(int[hit.j2+1]); ~ ^~~~~~~~ ~ ./hhalignment.C:1609:38: warning: when type is in parentheses, array cannot have dynamic size q->seq[q->nfirst]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:2690:38: warning: when type is in parentheses, array cannot have dynamic size I[N_in]=new(short unsigned int[L+2]); ~ ^~~ ~ ./hhalignment.C:2743:20: warning: when type is in parentheses, array cannot have dynamic size n = new(int*[L+2]); ~ ^~~ ~ ./hhalignment.C:2574:38: warning: when type is in parentheses, array cannot have dynamic size char* new_seq=new(char[2*maxcol]); ~ ^~~~~~~~ ~ ./hhalignment.C:2587:26: warning: when type is in parentheses, array cannot have dynamic size seq[N_in]=new(char[h]); ~ ^ ~ ./hhalignment.C:2590:24: warning: when type is in parentheses, array cannot have dynamic size X[N_in]=new(char[h]); ~ ^ ~ ./hhalignment.C:2592:38: warning: when type is in parentheses, array cannot have dynamic size I[N_in]=new(short unsigned int[h]); ~ ^ ~ ./hhalignment.C:2594:28: warning: when type is in parentheses, array cannot have dynamic size sname[N_in]=new(char[strlen(Tali.sname[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:2625:20: warning: when type is in parentheses, array cannot have dynamic size X[N_in]=new(char[L+2]); ~ ^~~ ~ ./hhhit.C./hhalignment.C::2522663::2026:: warningwarning: : when type is in parentheses, array cannot have dynamic sizewhen type is in parentheses, array cannot have dynamic size B_MM=new(double*[Nq]); seq[N_in]=new(char[L+2]); ~ ^~ ~ ~ ^~~ ~ ./hhhit.C:261:28./hhalignment.C: :warning2665: :when type is in parentheses, array cannot have dynamic size24 : warning: when type is in parentheses, array cannot have dynamic size B_MM[i] = new(double[Nt]); X[N_in]=new(char[L+2]); ~ ^~ ~ ~ ^~~ ~ ./hhhit.C:291:15: warning: when type is in parentheses, array cannot have dynamic size i = new(int[len]); ~ ^~~ ~ ./hhhit.C:292:15: warning: when type is in parentheses, array cannot have dynamic size j = new(int[len]); ~ ^~~ ~ ./hhalignment.C:2243:58: warning: add explicit braces to avoid dangling else [-Wdangling-else] if(in[k] && X[k][i]==GAP) wi[k]=wg[k]; else wi[k]=0.0; ^ ./hhalignment.C:1661:33: warning: when type is in parentheses, array cannot have dynamic size q->sname[nn]=new(char[strlen(sname[k])+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:1664:31: warning: when type is in parentheses, array cannot have dynamic size q->seq[nn]=new(char[strlen(seq[k])+1]); ~ ^~~~~~~~~~~~~~~~ ~ ./hhhmm.C./hhalignment.C:2177:28: warning: when type is in parentheses, array cannot have dynamic size char** lines = new(char*[3*L+100000]); ~ ^~~~~~~~~~ ~ ./hhhmm.C./hhalignment.C:2667:38: warning: when type is in parentheses, array cannot have dynamic size I[N_in]=new(short unsigned int[L+2]); ~ ^~~ ~ ./hhalignment.C:2686:26: warning: when type is in parentheses, array cannot have dynamic size seq[N_in]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:2688:24: warning: when type is in parentheses, array cannot have dynamic size X[N_in]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:1764:16: warning: when type is in parentheses, array cannot have dynamic size n = new(int*[L+2]); ~ ^~~ ~ ./hhalignment.C:2205:29: warning: when type is in parentheses, array cannot have dynamic size: 2690 lines[nline]=new(char[strlen(line)+1]);:38: warning ~ ^~~~~~~~~~~~~~ ~: when type is in parentheses, array cannot have dynamic size ./hhalignment.C:1826:57: warning: add explicit braces to avoid dangling else [-Wdangling-else] if(in[k] && X[k][i]0) wi[k]=wg[k]; else wi[k]=0.0; ^ ./hhalignment.C:2574:38: warning: when type is in parentheses, array cannot have dynamic size char* new_seq=new(char[2*maxcol]); ~ ^~~~~~~~ ~ ./hhalignment.C:2587:26: warning: when type is in parentheses, array cannot have dynamic size seq[N_in]=new(char[h]); ~ ^ ~ ./hhalignment.C:2329:30: warning: when type is in parentheses, array cannot have dynamic size seq[nss_pred]=new(char[L+2]); : ~ ^~~ ~ 2590 : 24./hhhmm.C: warning: when type is in parentheses, array cannot have dynamic size X[N_in]=new(char[h]); ~ ^ ~ ./hhalignment.C:2592:38: warning: when type is in parentheses, array cannot have dynamic size I[N_in]=new(short unsigned int[h]);:2336:30: ~ ^ ~warning : when type is in parentheses, array cannot have dynamic size ./hhalignment.C seq[nss_conf]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:2173:16: warning: when type is in parentheses, array cannot have dynamic size n = new(int*[L+2]); ~ ^~~ ~ In file included from :2594:28: warning: when type is in parentheses, array cannot have dynamic size sname[N_in]=new(char[strlen(Tali.sname[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:2243:58: warning: add explicit braces to avoid dangling else [-Wdangling-else] if(in[k] && X[k][i]==GAP) wi[k]=wg[k]; else wi[k]=0.0; ^ ./hhalignment.Chhconsensus.C:69: :./hhalignment.C2625::4720:: 21warning:: when type is in parentheses, array cannot have dynamic sizewarning : X[N_in]=new(char[L+2]);when type is in parentheses, array cannot have dynamic size sname = new(char*[maxseq+2]); ~ ^~~ ~ ~ ^~~~~~~~ ~./hhalignment.C ./hhalignment.C:48:19: warning: when type is in parentheses, array cannot have dynamic size seq = new(char*[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:49:15: warning: when type is in parentheses, array cannot have dynamic size l = new(int[maxres]); ~ ^~~~~~ ~ ./hhalignment.C:50:17./hhhit.C::1147:21: warning: when type is in parentheses, array cannot have dynamic size S = new( float[nsteps+1]); ~ ^~~~~~~~ ~ ./hhhit.C:1148:21: warning: when type is in parentheses, array cannot have dynamic size S_ss = new( float[nsteps+1]); ~ ^~~~~~~~ ~ warning: when type is in parentheses, array cannot have dynamic size X = new(char*[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C::512663::3126:: warningwarning: : when type is in parentheses, array cannot have dynamic sizewhen type is in parentheses, array cannot have dynamic size I = new(short unsigned int*[maxseq+2]); seq[N_in]=new(char[L+2]); ~ ^~~~~~~~ ~ ~ ^~~ ~ ./hhalignment.C./hhalignment.C:52:19: warning: :when type is in parentheses, array cannot have dynamic size2665 : keep = new(char[maxseq+2]);24: warning ~ ^~~~~~~~ ~: when type is in parentheses, array cannot have dynamic size X[N_in]=new(char[L+2]);./hhalignment.C ~ ^~~ ~ ./hhalignment.C:53:22: warning: when type is in parentheses, array cannot have dynamic size display = new(char[maxseq+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:2667:38::54 :warning18: :when type is in parentheses, array cannot have dynamic size warning I[N_in]=new(short unsigned int[L+2]);: when type is in parentheses, array cannot have dynamic size wg = new(float[maxseq+2]); ~ ^~~ ~ ~ ^~~~~~~~ ~ ./hhalignment.C ./hhalignment.C:55:19: warning: when type is in parentheses, array cannot have dynamic size nseqs = new(int[maxres+2]); ~ ^~~~~~~~ ~ ./hhalignment.C:2686:26: ./hhhit.C:1487:21: warning: when type is in parentheses, array cannot have dynamic size S = new( float[nsteps+1]); ~ ^~~~~~~~ ~ ./hhhit.C:1488:21: warning: when type is in parentheses, array cannot have dynamic size S_ss = new( float[nsteps+1]); ~ ^~~~~~~~ ~ ./hhhit.C:1489:28: warning: when type is in parentheses, array cannot have dynamic size P_posterior = new( float[nsteps+1]); ~ ^~~~~~~~ ~ warning: when type is in parentheses, array cannot have dynamic size seq[N_in]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:2688:24: warning: when type is in parentheses, array cannot have dynamic size X[N_in]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:144:20: warning: when type is in parentheses, array cannot have dynamic size nres=new(int[N_in]); ~ ^~~~ ~ ./hhalignment.C:2690:38: warning: when type is in parentheses, array cannot have dynamic size I[N_in]=new(short unsigned int[L+2]); ~ ^~~ ~ ./hhalignment.C:150:25: warning: when type is in parentheses, array cannot have dynamic size sname[k]=new(char[strlen(ali.sname[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:156:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(ali.seq[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:2743:20: warning: when type is in parentheses, array cannot have dynamic size n = new(int*[L+2]); ~ ^~~ ~ ./hhalignment.C:2430:28: warning: when type is in parentheses, array cannot have dynamic size char* cur_seq = new(char[par.maxcol]); // Sequence currently read in ~ ^~~~~~~~~~ ~ :162:21: warning: when type is in parentheses, array cannot have dynamic size ./hhalignment.C:2442:23: warning: when type is in parentheses, array cannot have dynamic size int* imatch=new(int[hit.j2+1]); ~ ^~~~~~~~ ~ X[k]=new(char[strlen(ali.seq[k])+2]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:167:35: warning: when type is in parentheses, array cannot have dynamic size I[k]=new(short unsigned int[strlen(ali.seq[k])+2]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhhit.C:1795:21: warning: when type is in parentheses, array cannot have dynamic size longname=new(char[strlen(t->longname)+1]); ~ ^~~~~~~~~~~~~~~~~~~~~ ~ ./hhhit.C:1796:21: warning: when type is in parentheses, array cannot have dynamic size name =new(char[strlen(t->name)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhhit.C:1797:21: warning: when type is in parentheses, array cannot have dynamic size file =new(char[strlen(t->file)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhhit.C:1808:22: warning: when type is in parentheses, array cannot have dynamic size this->i = new( int[i2+j2+2]); ~ ^~~~~~~ ~ ./hhhit.C:1809:22: warning: when type is in parentheses, array cannot have dynamic size this->j = new( int[i2+j2+2]); ~ ^~~~~~~ ~ ./hhhit.C:1810:23: warning: when type is in parentheses, array cannot have dynamic size states = new( char[i2+j2+2]); ~ ^~~~~~~ ~ ./hhhit.C:1813:19: warning: when type is in parentheses, array cannot have dynamic size sname=new(char*[t->n_display]); ~ ^~~~~~~~~~~~ ~ ./hhhit.C:1814:19: warning: when type is in parentheses, array cannot have dynamic size seq =new(char*[t->n_display]); ~ ^~~~~~~~~~~~ ~ ./hhalignment.C:2574:38: warning: when type is in parentheses, array cannot have dynamic size char* new_seq=new(char[2*maxcol]); ~ ^~~~~~~~ ~ ./hhalignment.C:2587:26: warning: when type is in parentheses, array cannot have dynamic size seq[N_in]=new(char[h]); ~ ^ ~ ./hhalignment.C:2590:24: warning: when type is in parentheses, array cannot have dynamic size X[N_in]=new(char[h]); ~ ^ ~ ./hhalignment.C:2592:38: warning: when type is in parentheses, array cannot have dynamic size I[N_in]=new(short unsigned int[h]); ~ ^ ~ ./hhalignment.C:2594:28: warning: when type is in parentheses, array cannot have dynamic size sname[N_in]=new(char[strlen(Tali.sname[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:2625:20: warning: when type is in parentheses, array cannot have dynamic size X[N_in]=new(char[L+2]); ~ ^~~ ~ In file included from hhblits.C:144: ./hhhit.C:141:17: warning: when type is in parentheses, array cannot have dynamic size bMM=new(char*[Nq]); ~ ^~ ~ ./hhhit.C:142:17: warning: when type is in parentheses, array cannot have dynamic size bMI=new(char*[Nq]); ~ ^~ ~ ./hhhit.C:143:17: warning./hhhit.C:1833:24: warning: when type is in parentheses, array cannot have dynamic size sname[k] = new(char[strlen(t->sname[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~~~ ~ ./hhhit.C: :1834:24: warning: when type is in parentheses, array cannot have dynamic size seq[k] = new(char[strlen(t->seq[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~ ~ when type is in parentheses, array cannot have dynamic size bIM=new(char*[Nq]); ./hhhit.C:1840:20: warning: when type is in parentheses, array cannot have dynamic size dbfile = new(char[strlen(ptr)+1]); ~ ^~~~~~~~~~~~~ ~ ~ ^~ ~ ./hhhit.C:144:17: warning: when type is in parentheses, array cannot have dynamic size bDG=new(char*[Nq]); ~ ^~ ~ ./hhalignment.C ./hhhit.C:145::25217::31 :warning warning: : when type is in parentheses, array cannot have dynamic sizewhen type is in parentheses, array cannot have dynamic size bGD=new(char*[Nq]); seq[k]=new(char[strlen(cur_seq)+2]); ~ ^~ ~ ~ ^~~~~~~~~~~~~~~~~ ~ ./hhhit.C ./hhalignment.C:146:22: warning: when type is in parentheses, array cannot have dynamic size cell_off=new(char*[Nq]);: 254 ~ ^~ ~: 29 : ./hhhit.Cwarning: when type is in parentheses, array cannot have dynamic size X[k]=new(char[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:256:43: warning: when type is in parentheses, array cannot have dynamic size I[k]=new(short unsigned int[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:2663:26: warning: when type is in parentheses, array cannot have dynamic size seq[N_in]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:2665:24: warning: when type is in parentheses, array cannot have dynamic size X[N_in]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:2667:38: warning: when type is in parentheses, array cannot have dynamic size I[N_in]=new(short unsigned int[L+2]); ~ ^~~ ~ ./hhalignment.C:2686:26: warning: when type is in parentheses, array cannot have dynamic size seq[N_in]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:2688:24: warning: when type is in parentheses, array cannot have dynamic size X[N_in]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:2690:38: warning: when type is in parentheses, array cannot have dynamic size I[N_in]=new(short unsigned int[L+2]); ~ ^~~ ~ ./hhalignment.C:315:31: warning: when type is in parentheses, array cannot have dynamic size sname[k] = new(char[strlen(cur_name)+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:2743:20: warning: when type is in parentheses, array cannot have dynamic size n = new(int*[L+2]); ~ ^~~ ~ :149:23: warning: when type is in parentheses, array cannot have dynamic size bMM[i]=new(char[Nt]); ~ ^~ ~ ./hhhit.C:150:23: warning: when type is in parentheses, array cannot have dynamic size bMI[i]=new(char[Nt]); ~ ^~ ~ ./hhhit.C:151:23: warning: when type is in parentheses, array cannot have dynamic size bIM[i]=new(char[Nt]); ~ ^~ ~ ./hhhit.C:152:23: warning: when type is in parentheses, array cannot have dynamic size bGD[i]=new(char[Nt]); ~ ^~ ~ ./hhhit.C:153:23: warning: when type is in parentheses, array cannot have dynamic size bDG[i]=new(char[Nt]); ~ ^~ ~ ./hhhit.C:154:28: warning: when type is in parentheses, array cannot have dynamic size cell_off[i]=new(char[Nt]); ~ ^~ ~ ./hhhit.C:192:20: warning: when type is in parentheses, array cannot have dynamic size F_MM=new(double*[Nq]); ~ ^~ ~ ./hhhit.C:199:20: warning: when type is in parentheses, array cannot have dynamic size scale=new(double[Nq+1]); // need Nq+3? ~ ^~~~ ~ ./hhhit.C:202:28: warning: when type is in parentheses, array cannot have dynamic size F_MM[i] = new(double[Nt]); ~ ^~ ~ ./hhhit.C:252:20: warning: when type is in parentheses, array cannot have dynamic size B_MM=new(double*[Nq]); ~ ^~ ~ ./hhhit.C:261:28: warning: when type is in parentheses, array cannot have dynamic size B_MM[i] = new(double[Nt]); ~ ^~ ~ In file included from hhsearch.C:114: ./hhhit.C:141:17: warning: when type is in parentheses, array cannot have dynamic size bMM=new(char*[Nq]); ~ ^~ ~ ./hhhit.C:142:17: warning: when type is in parentheses, array cannot have dynamic size bMI=new(char*[Nq]); ~ ^~ ~ ./hhhit.C:143:17: warning: when type is in parentheses, array cannot have dynamic size bIM=new(char*[Nq]); ~ ^~ ~ ./hhhit.C:144:17: warning: when type is in parentheses, array cannot have dynamic size bDG=new(char*[Nq]); ~ ^~ ~ ./hhhit.C:145:17: warning: when type is in parentheses, array cannot have dynamic size bGD=new(char*[Nq]); ~ ^~ ~ ./hhhit.C:146:22: warning: when type is in parentheses, array cannot have dynamic size cell_off=new(char*[Nq]); ~ ^~ ~ ./hhhit.C:149:23: warning: when type is in parentheses, array cannot have dynamic size bMM[i]=new(char[Nt]); ~ ^~ ~ ./hhhit.C:150:23: warning: when type is in parentheses, array cannot have dynamic size bMI[i]=new(char[Nt]); ~ ^~ ~ ./hhhit.C:151:23: warning: when type is in parentheses, array cannot have dynamic size bIM[i]=new(char[Nt]); ~ ^~ ~ ./hhhit.C:291:15: warning: when type is in parentheses, array cannot have dynamic size i = new(int[len]); ~ ^~~ ~ ./hhhit.C:292:15: warning: when type is in parentheses, array cannot have dynamic size j = new(int[len]); ~ ^~~ ~ In file included from hhalign.C:98: ./hhhalfalignment.C:46:15: warning: when type is in parentheses, array cannot have dynamic size h = new(int[maxseqdis]); //h[k] = next position of sequence k to be written ~ ^~~~~~~~~ ~ ./hhhalfalignment.C:47:17: warning: when type is in parentheses, array cannot have dynamic size s = new(char*[maxseqdis]); //s[k][h] = character in column h, sequence k of output alignment ~ ^~~~~~~~~ ~ ./hhhalfalignment.C:48:16: warning: when type is in parentheses, array cannot have dynamic size l = new(int*[maxseqdis]); //counts non-gap residues: l[k][i] = index of last residue AT OR BEFORE match state i in seq k ~ ^~~~~~~~~ ~ ./hhhalfalignment.C:49:16: warning: when type is in parentheses, array cannot have dynamic size m = new(int*[maxseqdis]); //counts positions: m[k][i] = position of match state i in string seq[k] ~ ^~~~~~~~~ ~ ./hhhit.C:152:23: warning: when type is in parentheses, array cannot have dynamic size bGD[i]=new(char[Nt]); ~ ^~ ~ ./hhhit.C:153:23: warning: when type is in parentheses, array cannot have dynamic size bDG[i]=new(char[Nt]); ~ ^~ ~ ./hhhit.C:154:28: warning: when type is in parentheses, array cannot have dynamic size cell_off[i]=new(char[Nt]); ~ ^~ ~ ./hhhit.C:192:20: warning: when type is in parentheses, array cannot have dynamic size F_MM=new(double*[Nq]); ~ ^~ ~ ./hhhit.C:199:20: warning: when type is in parentheses, array cannot have dynamic size scale=new(double[Nq+1]); // need Nq+3? ~ ^~~~ ~ ./hhhit.C:202:28: warning: when type is in parentheses, array cannot have dynamic size F_MM[i] = new(double[Nt]); ~ ^~ ~ ./hhhit.C:252:20: warning: when type is in parentheses, array cannot have dynamic size B_MM=new(double*[Nq]); ~ ^~ ~ ./hhhit.C:261:28: warning: when type is in parentheses, array cannot have dynamic size B_MM[i] = new(double[Nt]); ~ ^~ ~ ./hhhit.C:291:15: warning: when type is in parentheses, array cannot have dynamic size i = new(int[len]); ~ ^~~ ~ ./hhhit.C:292:15: warning: when type is in parentheses, array cannot have dynamic size j = new(int[len]); ~ ^~~ ~ 99 warnings and 1 error generated. ./hhhit.C./hhalignment.C:1147:21: warning: when type is in parentheses, array cannot have dynamic size S = new( float[nsteps+1]); ~ ^~~~~~~~ ~ ./hhhit.C:1148:21: warning: when type is in parentheses, array cannot have dynamic size S_ss = new( float[nsteps+1]); ~ ^~~~~~~~ ~ :431:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:433:21: warning: when type is in parentheses, array cannot have dynamic size X[k]=new(char[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:435:35: warning: when type is in parentheses, array cannot have dynamic size I[k]=new(short unsigned int[strlen(cur_seq)+2]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhhit.C:1147:21: warning: when type is in parentheses, array cannot have dynamic size S = new( float[nsteps+1]); ~ ^~~~~~~~ ~ ./hhhit.C:1148:21: warning: when type is in parentheses, array cannot have dynamic size S_ss = new( float[nsteps+1]); ~ ^~~~~~~~ ~ ./hhhit.C:1487:21: warning: when type is in parentheses, array cannot have dynamic size S = new( float[nsteps+1]); ~ ^~~~~~~~ ~ ./hhhit.C:1488:21: warning: when type is in parentheses, array cannot have dynamic size S_ss = new( float[nsteps+1]); ~ ^~~~~~~~ ~ ./hhhit.C:1489:28: warning: when type is in parentheses, array cannot have dynamic size P_posterior = new( float[nsteps+1]); ~ ^~~~~~~~ ~ make[2]: *** [hhfilter] Error 1 Makefile:119: recipe for target 'hhfilter' failed ./hhhit.C:1487:21: warning: when type is in parentheses, array cannot have dynamic size S = new( float[nsteps+1]); ~ ^~~~~~~~ ~ ./hhhit.C:1488:21: warning: when type is in parentheses, array cannot have dynamic size S_ss = new( float[nsteps+1]); ~ ^~~~~~~~ ~ ./hhhit.C:1489:28: warning: when type is in parentheses, array cannot have dynamic size P_posterior = new( float[nsteps+1]); ~ ^~~~~~~~ ~ ./hhhit.C:1795:21: warning: when type is in parentheses, array cannot have dynamic size longname=new(char[strlen(t->longname)+1]); ~ ^~~~~~~~~~~~~~~~~~~~~ ~ ./hhhit.C:1796:21: warning: when type is in parentheses, array cannot have dynamic size name =new(char[strlen(t->name)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhhit.C:1797:21: warning: when type is in parentheses, array cannot have dynamic size file =new(char[strlen(t->file)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhhit.C:1795:21: warning: when type is in parentheses, array cannot have dynamic size longname=new(char[strlen(t->longname)+1]); ~ ^~~~~~~~~~~~~~~~~~~~~ ~ ./hhhit.C:1796:21: warning: when type is in parentheses, array cannot have dynamic size ./hhhit.C:1808:22: warning: when type is in parentheses, array cannot have dynamic size this->i = new( int[i2+j2+2]); ~ ^~~~~~~ ~ ./hhhit.C:1809:22: warning: when type is in parentheses, array cannot have dynamic size this->j = new( int[i2+j2+2]); ~ ^~~~~~~ ~ ./hhhit.C:1810:23: warning: when type is in parentheses, array cannot have dynamic size states = new( char[i2+j2+2]); ~ ^~~~~~~ ~ ./hhhit.C name =new(char[strlen(t->name)+1]);:1813:19: warning: when type is in parentheses, array cannot have dynamic size sname=new(char*[t->n_display]); ~ ^~~~~~~~~~~~ ~ ./hhhit.C:1814:19: warning: when type is in parentheses, array cannot have dynamic size seq =new(char*[t->n_display]); ~ ^~~~~~~~~~~~ ~ ~ ^~~~~~~~~~~~~~~~~ ~ ./hhhit.C:1833:24: warning: when type is in parentheses, array cannot have dynamic size sname[k] = new(char[strlen(t->sname[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~~~ ~ ./hhhit.C:1834:24: warning: when type is in parentheses, array cannot have dynamic size seq[k] = new(char[strlen(t->seq[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~ ~ ./hhhit.C:1797:21./hhhit.C:1840:20: warning: when type is in parentheses, array cannot have dynamic size dbfile = new(char[strlen(ptr)+1]); ~ ^~~~~~~~~~~~~ ~ : warning: when type is in parentheses, array cannot have dynamic size file =new(char[strlen(t->file)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhhit.C:1808:22: warning: when type is in parentheses, array cannot have dynamic size this->i = new( int[i2+j2+2]); ~ ^~~~~~~ ~ ./hhhit.C./hhalignment.C:649:31: warning: when type is in parentheses, array cannot have dynamic size if (nres==NULL) nres=new(int[N_in]); ~ ^~~~ ~ :1809:22: warning: when type is in parentheses, array cannot have dynamic size this->j = new( int[i2+j2+2]); ~ ^~~~~~~ ~ ./hhhit.C:1810:23: warning: when type is in parentheses, array cannot have dynamic size states = new( char[i2+j2+2]); ~ ^~~~~~~ ~ ./hhhit.C:1813:19: warning: when type is in parentheses, array cannot have dynamic size sname=new(char*[t->n_display]); ~ ^~~~~~~~~~~~ ~ ./hhhit.C:1814:19: warning: when type is in parentheses, array cannot have dynamic size seq =new(char*[t->n_display]); ~ ^~~~~~~~~~~~ ~ ./hhhit.C:1833:24: warning: when type is in parentheses, array cannot have dynamic size sname[k] = new(char[strlen(t->sname[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~~~ ~ ./hhhit.C:1834:24: warning: when type is in parentheses, array cannot have dynamic size seq[k] = new(char[strlen(t->seq[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~ ~ ./hhhit.C:1840:20: warning: when type is in parentheses, array cannot have dynamic size dbfile = new(char[strlen(ptr)+1]); ~ ^~~~~~~~~~~~~ ~ In file included from In file included from hhblits.C:145: ./hhhalfalignment.C:46:15: warning: when type is in parentheses, array cannot have dynamic size h = new(int[maxseqdis]); //h[k] = next position of sequence k to be written ~ ^~~~~~~~~ ~ ./hhhalfalignment.C:47:17: warning: when type is in parentheses, array cannot have dynamic size s = new(char*[maxseqdis]); //s[k][h] = character in column h, sequence k of output alignment ~ ^~~~~~~~~ ~ ./hhhalfalignment.C:48:16: warning: when type is in parentheses, array cannot have dynamic size l = new(int*[maxseqdis]); //counts non-gap residues: l[k][i] = index of last residue AT OR BEFORE match state i in seq k ~ ^~~~~~~~~ ~ ./hhhalfalignment.C:49:16: warning: when type is in parentheses, array cannot have dynamic size m = new(int*[maxseqdis]); //counts positions: m[k][i] = position of match state i in string seq[k] ~ ^~~~~~~~~ ~ hhsearch.C:115: ./hhhalfalignment.C:46:15: warning: when type is in parentheses, array cannot have dynamic size h = new(int[maxseqdis]); //h[k] = next position of sequence k to be written ~ ^~~~~~~~~ ~ ./hhhalfalignment.C:47:17: warning: when type is in parentheses, array cannot have dynamic size s = new(char*[maxseqdis]); //s[k][h] = character in column h, sequence k of output alignment ~ ^~~~~~~~~ ~ ./hhhalfalignment.C:48:16: warning: when type is in parentheses, array cannot have dynamic size l = new(int*[maxseqdis]); //counts non-gap residues: l[k][i] = index of last residue AT OR BEFORE match state i in seq k ~ ^~~~~~~~~ ~ ./hhhalfalignment.C:49:16: warning: when type is in parentheses, array cannot have dynamic size m = new(int*[maxseqdis]); //counts positions: m[k][i] = position of match state i in string seq[k] ~ ^~~~~~~~~ ~ ./hhalignment.C:923:23: warning: when type is in parentheses, array cannot have dynamic size seq[k]=new(char[strlen(q->seq[qk])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:926:21: warning: when type is in parentheses, array cannot have dynamic size X[k]=new(char[strlen(q->seq[qk])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:928:35: warning: when type is in parentheses, array cannot have dynamic size I[k]=new(short unsigned int[strlen(q->seq[qk])+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~ 99 warnings and 1 error generated. ./hhalignment.C:949:27: warning: when type is in parentheses, array cannot have dynamic size sname[k] = new(char[strlen(q->sname[qk])+1]); ~ ^~~~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:972:26: warning: when type is in parentheses, array cannot have dynamic size char *dummy = new(char[N_in+1]); ~ ^~~~~~ ~ ./hhalignment.C:1031:21: warning: when type is in parentheses, array cannot have dynamic size char* in=new(char[N_in+1]); // in[k]=1: seq k has been accepted; in[k]=0: seq k has not yet been accepted at current seqid ~ ^~~~~~ ~ ./hhalignment.C:1032:23: warning: when type is in parentheses, array cannot have dynamic size char* inkk=new(char[N_in+1]); // inkk[k]=1 iff in[ksort[k]]=1 else 0; ~ ^~~~~~ ~ ./hhalignment.C:1033:21: warning: when type is in parentheses, array cannot have dynamic size int* Nmax=new(int[L+2]); // position-dependent maximum-sequence-identity threshold for filtering? (variable used in former version was idmax) ~ ^~~ ~ ./hhalignment.C:1034:25: warning: when type is in parentheses, array cannot have dynamic size int* idmaxwin=new(int[L+2]); // minimum value of idmax[i-WFIL,i+WFIL] ~ ^~~ ~ ./hhalignment.C:1035:27: warning: when type is in parentheses, array cannot have dynamic size int* seqid_prev=new(int[N_in+1]); // maximum-sequence-identity threshold used in previous round of filtering (with lower seqid) ~ ^~~~~~ ~ ./hhalignment.C:1036:18: warning: when type is in parentheses, array cannot have dynamic size int* N=new(int[L+2]); // N[i] number of already accepted sequences at position i ~ ^~~ ~ ./hhalignment.C:1064:21: warning: when type is in parentheses, array cannot have dynamic size first=new(int[N_in]);// first non-gap position in sequence k ~ ^~~~ ~ ./hhalignment.C:1065:21: warning: when type is in parentheses, array cannot have dynamic size last =new(int[N_in]);// last non-gap position in sequence k ~ ^~~~ ~ ./hhalignment.C:1079:20: warning: when type is in parentheses, array cannot have dynamic size nres=new(int[N_in]); ~ ^~~~ ~ ./hhalignment.C:1095:21: warning: when type is in parentheses, array cannot have dynamic size ksort=new(int[N_in]); // never reuse alignment object for new alignment with more sequences ~ ^~~~ ~ make[2]: *** [hhmake] Error 1 Makefile:104: recipe for target 'hhmake' failed ./hhalignment.C:1303:30: warning: when type is in parentheses, array cannot have dynamic size float** logodds=new(float*[L+1]); // log-odds ratios for HMM qcore ~ ^~~ ~ ./hhalignment.C:1312:21: warning: when type is in parentheses, array cannot have dynamic size first=new(int[N_in]);// first non-gap position in sequence k ~ ^~~~ ~ ./hhalignment.C:1313:21: warning: when type is in parentheses, array cannot have dynamic size last =new(int[N_in]);// last non-gap position in sequence k ~ ^~~~ ~ ./hhalignment.C:1326:20: warning: when type is in parentheses, array cannot have dynamic size nres=new(int[N_in]); ~ ^~~~ ~ ./hhalignment.C:1598:37: warning: when type is in parentheses, array cannot have dynamic size q->seq[q->ncons]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:1605:40: warning: when type is in parentheses, array cannot have dynamic size q->sname[q->nfirst]=new(char[strlen(name)+11]); ~ ^~~~~~~~~~~~~~~ ~ ./hhalignment.C:1609:38: warning: when type is in parentheses, array cannot have dynamic size q->seq[q->nfirst]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:1661:33: warning: when type is in parentheses, array cannot have dynamic size q->sname[nn]=new(char[strlen(sname[k])+1]); ~ ^~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:1664:31: warning: when type is in parentheses, array cannot have dynamic size q->seq[nn]=new(char[strlen(seq[k])+1]); ~ ^~~~~~~~~~~~~~~~ ~ ./hhalignment.C:1764:16: warning: when type is in parentheses, array cannot have dynamic size n = new(int*[L+2]); ~ ^~~ ~ ./hhalignment.C:1826:57: warning: add explicit braces to avoid dangling else [-Wdangling-else] if(in[k] && X[k][i]0) wi[k]=wg[k]; else wi[k]=0.0; ^ ./hhalignment.C:2173:16: warning: when type is in parentheses, array cannot have dynamic size n = new(int*[L+2]); ~ ^~~ ~ ./hhalignment.C:2243:58: warning: add explicit braces to avoid dangling else [-Wdangling-else] if(in[k] && X[k][i]==GAP) wi[k]=wg[k]; else wi[k]=0.0; ^ ./hhalignment.C:2430:28: warning: when type is in parentheses, array cannot have dynamic size char* cur_seq = new(char[par.maxcol]); // Sequence currently read in ~ ^~~~~~~~~~ ~ ./hhalignment.C:2442:23: warning: when type is in parentheses, array cannot have dynamic size int* imatch=new(int[hit.j2+1]); ~ ^~~~~~~~ ~ ./hhalignment.C:2574:38: warning: when type is in parentheses, array cannot have dynamic size char* new_seq=new(char[2*maxcol]); ~ ^~~~~~~~ ~ ./hhalignment.C:2587:26: warning: when type is in parentheses, array cannot have dynamic size seq[N_in]=new(char[h]); ~ ^ ~ ./hhalignment.C:2590:24: warning: when type is in parentheses, array cannot have dynamic size X[N_in]=new(char[h]); ~ ^ ~ ./hhalignment.C:2592:38: warning: when type is in parentheses, array cannot have dynamic size I[N_in]=new(short unsigned int[h]); ~ ^ ~ ./hhalignment.C:2594:28: warning: when type is in parentheses, array cannot have dynamic size sname[N_in]=new(char[strlen(Tali.sname[k])+1]); ~ ^~~~~~~~~~~~~~~~~~~~~~~ ~ ./hhalignment.C:2625:20: warning: when type is in parentheses, array cannot have dynamic size X[N_in]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:2663:26: warning: when type is in parentheses, array cannot have dynamic size seq[N_in]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:2665:24: warning: when type is in parentheses, array cannot have dynamic size X[N_in]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:2667:38: warning: when type is in parentheses, array cannot have dynamic size I[N_in]=new(short unsigned int[L+2]); ~ ^~~ ~ ./hhalignment.C:2686:26: warning: when type is in parentheses, array cannot have dynamic size seq[N_in]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:2688:24: warning: when type is in parentheses, array cannot have dynamic size X[N_in]=new(char[L+2]); ~ ^~~ ~ ./hhalignment.C:2690:38: warning: when type is in parentheses, array cannot have dynamic size I[N_in]=new(short unsigned int[L+2]); ~ ^~~ ~ ./hhalignment.C:2743:20: warning: when type is in parentheses, array cannot have dynamic size n = new(int*[L+2]); ~ ^~~ ~ In file included from hhconsensus.C:70: ./hhhalfalignment.C:46:15: warning: when type is in parentheses, array cannot have dynamic size h = new(int[maxseqdis]); //h[k] = next position of sequence k to be written ~ ^~~~~~~~~ ~ ./hhhalfalignment.C:47:17: warning: when type is in parentheses, array cannot have dynamic size s = new(char*[maxseqdis]); //s[k][h] = character in column h, sequence k of output alignment ~ ^~~~~~~~~ ~ ./hhhalfalignment.C:48:16: warning: when type is in parentheses, array cannot have dynamic size l = new(int*[maxseqdis]); //counts non-gap residues: l[k][i] = index of last residue AT OR BEFORE match state i in seq k ~ ^~~~~~~~~ ~ ./hhhalfalignment.C:49:16: warning: when type is in parentheses, array cannot have dynamic size m = new(int*[maxseqdis]); //counts positions: m[k][i] = position of match state i in string seq[k] ~ ^~~~~~~~~ ~ hhsearch.C:375:38: warning: when type is in parentheses, array cannot have dynamic size par.dbfiles = new(char[strlen(argv[i])+1]); ~ ^~~~~~~~~~~~~~~~~ ~ hhsearch.CIn file included from hhblits.C:262: ./hhprefilter.C:794:34: warning: when type is in parentheses, array cannot have dynamic size dbfiles_new[ndb_new]=new(char[strlen(db_name)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ In file included from :445:34: warning: hhalign.Cwhen type is in parentheses, array cannot have dynamic size: 105 par.exclstr = new(char[strlen(argv[i])+1]);: ./pngwriter.cc:640: 19 ~ ^~~~~~~~~~~~~~~~~ ~ : warning: equality comparison with extraneous parentheses [-Wparentheses-equality] if((bit_depth_ == 16)) ~~~~~~~~~~~^~~~~ ./pngwriter.cc:640:19: note: remove extraneous parentheses around the comparison to silence this warning if((bit_depth_ == 16)) ~ ^ ~ ./pngwriter.cc:640:19: note: use '=' to turn this equality comparison into an assignment if((bit_depth_ == 16)) ^~ = ./pngwriter.cc:663:19: warning: equality comparison with extraneous parentheses [-Wparentheses-equality] if((bit_depth_ == 8)) ~~~~~~~~~~~^~~~ ./pngwriter.cc:663:19: note: remove extraneous parentheses around the comparison to silence this warning if((bit_depth_ == 8)) ~ ^ ~ ./pngwriter.cc:663:19: note: use '=' to turn this equality comparison into an assignment if((bit_depth_ == 8)) ^~ = ./pngwriter.cc./hhprefilter.C:846:30: warning: when type is in parentheses, array cannot have dynamic size dbnames[num_dbs]=new(char[strlen(word)+1]); ~ ^~~~~~~~~~~~~~ ~ ./hhprefilter.C:1045:38: warning: when type is in parentheses, array cannot have dynamic size __m128i** workspace = new(__m128i*[cpu]); ~ ^~~ ~ :886:35: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare] if((index > 999999999)||(index < 0)) ~~~~~ ^ ~ ./hhprefilter.C:1144:38: warning: when type is in parentheses, array cannot have dynamic size dbfiles_old[ndb_old]=new(char[strlen(db_name)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ ./hhprefilter.C:1150:38: warning: when type is in parentheses, array cannot have dynamic size dbfiles_new[ndb_new]=new(char[strlen(db_name)+1]); ~ ^~~~~~~~~~~~~~~~~ ~ hhsearch.C:672:32: warning: when type is in parentheses, array cannot have dynamic size Qali.longname = new(char[strlen(q->longname)+1]); ~ ^~~~~~~~~~~~~~~~~~~~~ ~ hhsearch.C:705:32: warning: when type is in parentheses, array cannot have dynamic size hit[bin]->dbfile = new(char[strlen(hit_cur.dbfile)+1]); ~ ^~~~~~~~~~~~~~~~~~~~~~~~ ~ hhsearch.C:963:36: warning: when type is in parentheses, array cannot have dynamic size hit[bin]->dbfile = new(char[strlen(dbfiles[idb])+1]); ~ ^~~~~~~~~~~~~~~~~~~~~~ ~ hhsearch.C:1268:20: warning: when type is in parentheses, array cannot have dynamic size format = new(int[bins]); ~ ^~~~ ~ hhsearch.C:1304:45: warning: when type is in parentheses, array cannot have dynamic size dbfiles[ndb]=new(char[strlen(dbfile)+1]); ~ ^~~~~~~~~~~~~~~~ ~ hhsearch.C:1317:37: warning: when type is in parentheses, array cannot have dynamic size dbfiles[ndb]=new(char[strlen(dbfile_cur)+1]); ~ ^~~~~~~~~~~~~~~~~~~~ ~103 warnings and 1 error generated. hhsearch.Chhblits.C:781:32: warning: when type is in parentheses, array cannot have dynamic size Qali.longname = new(char[strlen(q->longname)+1]); ~ ^~~~~~~~~~~~~~~~~~~~~ ~ :1433:43: warning: when type is in parentheses, array cannot have dynamic size hit[bin]->dbfile = new(char[strlen(dbfiles[idb])+1]); ~ ^~~~~~~~~~~~~~~~~~~~~~ ~ hhblits.C:914:32: warning: when type is in parentheses, array cannot have dynamic size hit[bin]->dbfile = new(char[strlen(dbfiles[idb])+1]); ~ ^~~~~~~~~~~~~~~~~~~~~~ ~ make[2]: *** [hhconsensus] Error 1 Makefile:128: recipe for target 'hhconsensus' failed hhblits.C:1120:26: warning: when type is in parentheses, array cannot have dynamic size dbfiles[ndb]=new(char[strlen(hit_cur.dbfile)+1]); ~ ^~~~~~~~~~~~~~~~~~~~~~~~ ~ hhblits.C:1406:32: warning: when type is in parentheses, array cannot have dynamic size hit[bin]->dbfile = new(char[strlen(hit_cur.dbfile)+1]); ~ ^~~~~~~~~~~~~~~~~~~~~~~~ ~ hhblits.C:1716:36: warning: when type is in parentheses, array cannot have dynamic size hit[bin]->dbfile = new(char[strlen(dbfiles[idb])+1]); ~ ^~~~~~~~~~~~~~~~~~~~~~ ~ hhblits.C:2140:20: warning: when type is in parentheses, array cannot have dynamic size format = new(int[bins]); ~ ^~~~ ~ hhblits.C:2240:33: warning: when type is in parentheses, array cannot have dynamic size dbfiles_new[ndb_new]=new(char[strlen(dbfiles_old[a])+1]); ~ ^~~~~~~~~~~~~~~~~~~~~~~~ ~ hhalign.C:442:27: warning: when type is in parentheses, array cannot have dynamic size pngfile = new(char[strlen(argv[i])+1]); ~ ^~~~~~~~~~~~~~~~~ ~ hhalign.C:452:29: warning: when type is in parentheses, array cannot have dynamic size strucfile = new(char[strlen(argv[i])+1]); ~ ^~~~~~~~~~~~~~~~~ ~ hhalign.C:474:26: warning: when type is in parentheses, array cannot have dynamic size tcfile = new(char[strlen(argv[i])+1]); ~ ^~~~~~~~~~~~~~~~~ ~ hhalign.C:491:27: warning: when type is in parentheses, array cannot have dynamic size par.exclstr = new(char[strlen(argv[i])+1]); ~ ^~~~~~~~~~~~~~~~~ ~ hhalign.C:539:28: warning: when type is in parentheses, array cannot have dynamic size dmapfile = new(char[strlen(argv[i])+1]); ~ ^~~~~~~~~~~~~~~~~ ~ 147 warnings and 1 error generated. make[2]: *** [hhsearch] Error 1 Makefile:86: recipe for target 'hhsearch' failed hhalign.C:943:27: warning: when type is in parentheses, array cannot have dynamic size Pstruc = new(float*[q->L+2]); ~ ^~~~~~ ~ hhalign.C:944:58: warning: when type is in parentheses, array cannot have dynamic size for (int i=0; iL+2; i++) Pstruc[i] = new(float[t->L+2]); ~ ^~~~~~ ~ hhalign.C:945:27: warning: when type is in parentheses, array cannot have dynamic size Sstruc = new(float*[q->L+2]); ~ ^~~~~~ ~ hhalign.C:946:58: warning: when type is in parentheses, array cannot have dynamic size for (int i=0; iL+2; i++) Sstruc[i] = new(float[t->L+2]); ~ ^~~~~~ ~ hhalign.C:1182:28: warning: when type is in parentheses, array cannot have dynamic size float** s=new(float*[q->L+2]); ~ ^~~~~~ ~ hhalign.C:1184:22: warning: when type is in parentheses, array cannot have dynamic size if(!(s[i]=new(float[t->L+2]))) MemoryError("image map"); ~ ^~~~~~ ~ hhalign.C:1220:23: warning: when type is in parentheses, array cannot have dynamic size ali = new(int*[q->L+2]); ~ ^~~~~~ ~ hhalign.C:1223:22: warning: when type is in parentheses, array cannot have dynamic size ali[i] = new(int[t->L+2]); ~ ^~~~~~ ~ hhalign.C:1229:26: warning: when type is in parentheses, array cannot have dynamic size alisto = new(int*[q->L+2]); ~ ^~~~~~ ~ hhalign.C:1232:25: warning: when type is in parentheses, array cannot have dynamic size alisto[i] = new(int[t->L+2]); ~ ^~~~~~ ~ 150 warnings and 1 error generated. make[2]: *** [hhblits] Error 1 Makefile:95: recipe for target 'hhblits' failed 156 warnings and 1 error generated. make[2]: *** [hhalign] Error 1 Makefile:110: recipe for target 'hhalign' failed make[2]: Leaving directory '/«PKGBUILDDIR»/src' make[1]: *** [all] Error 2 dh_auto_build: make -j10 returned exit code 2 Makefile:21: recipe for target 'all' failed make[1]: Leaving directory '/«PKGBUILDDIR»' make: *** [build-arch] Error 2 dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2 debian/rules:46: recipe for target 'build-arch' failed ──────────────────────────────────────────────────────────────────────────────── Build finished at 20140617-1316 Finished ──────── E: Build failure (dpkg-buildpackage died) ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /«BUILDDIR» Not cleaning session: cloned chroot in use ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Build Architecture: amd64 Build-Space: 13204 Build-Time: 13 Distribution: unstable Fail-Stage: build Host Architecture: amd64 Install-Time: 10 Job: hhsuite_2.0.16-1 Machine Architecture: amd64 Package: hhsuite Package-Time: 56 Source-Version: 2.0.16-1 Space: 13204 Status: attempted Version: 2.0.16-1clang1 ──────────────────────────────────────────────────────────────────────────────── Finished at 20140617-1316 Build needed 00:00:56, 13204k disc space DC-Status: Failed 57.508633668s DC-Time-Estimation: 57.508633668 versus expected 597 (r/m: 9.381049973235472 ; m: 57.508633668)